Almost two years have passed since the First Alliance-PLANT War between the Earth Alliance and the PLANT space colonies ended with the Treaty of Junius Seven. The treaty placed restrictions on the numbers of mobile suits that could be maintained, and nuclear technology such as nuclear weapons, N-Jammers and N-Jammer Cancellers, as well as Mirage Colloid were banned outright.
ZAFT, the PLANT's military organization, provided N-Jammer Cancellers to the Earth Alliance to solve its energy crisis, caused by the "April's Fool" attack on Earth, in which ZAFT buried N-Jammers deep underground to prevent any further nuclear attacks on PLANT, as well as killing millions of people on Earth that were completely reliant on nuclear power found themselves without electricity. All political power and territories taken by the Earth Alliance during the war, especially the neutral nation of the Orb Union but also the United States of South America, was to be returned to the respective government of the countries.
The Treaty of Junius Seven failed to ban the anti-Coordinator factions on Earth. Thus, in those two years, one of the primary forces behind the war, the ruling extremist Earth Alliance organization Blue Cosmos, reorganized under the leadership of Lord Djibril, and continued to exercise influence over Earth's political elite.
Peace treaty notwithstanding, both PLANT/ZAFT and Earth Alliance continued to expand their military assets, including development of new mobile suit units. Even if nuclear technologies were banned, some of it remained secretly on their development agendas.
The Armory One Incident (October 2, C.E. 73)
With both PLANT/ZAFT and Earth Alliance members building up their military powers, Orb Union representative Cagalli Yula Athha arranged a meeting with PLANT chairman Gilbert Durandal to discuss the need for power in the post-war era. Athrun Zala accompanied her as a bodyguard, under the alias "Alex Dino". The meeting took place at ZAFT's Armory One, which was currently preparing for the launch ceremony of the first post-war battleship, the Minerva.
While Cagalli met with Durandal, Earth Alliance pilots Sting Oakley, Stella Loussier, and Auel Neider infiltrated the base, commandeered ZAFT's newest Gundam-type mobile suits, the ZGMF-X24S Chaos Gundam, ZGMF-X31S Abyss Gundam, and ZGMF-X88S Gaia Gundam, and heavily damaged the installation as they attempted to escape the base.
Various ZAFT mobile suits engaged the three units, including the new Zaku Warrior/Phantom units and the ZGMF-X56S Impulse Gundam, piloted by Shinn Asuka, as well as the crew of the Minerva. The stolen units successfully escaped the colony, and were picked up by the Mirage Colloid-cloaked Earth Alliance battleship Girty Lue, waiting just outside the colony.
The Minerva launched and chased the Girty Lue, engaging in battle several times. The chase was interrupted when the Minerva was involved in the upcoming Junius Seven Colony Drop Incident, which would become known as Operation: "Break the World".
Junius Seven Colony Drop Incident - Operation: "Break The World"
The theft of the three Gundams was immediately set aside when movement was detected from Junius Seven, which was supposed to be in a stable orbit. A rogue ZAFT force that supported the late Patrick Zala and piloting ZGMF-1017M2 GINN High Maneuver Type II units, planted engines all over the colony's remains, sending it on a collision course with Earth.
A ZAFT squadron under the command of Yzak Joule was dispatched to break up the colony, and was soon reinforced by the approaching Minerva's mobile suits. They were engaged in close combat battle by the rogue squadron, who (mostly) easily outperformed the members of the Joule team, and operations to break Junius Seven into pieces were compromised. The Girty Lue also arrived on the scene, launched the stolen mobile suit units and engaged the Minerva, further hampering operations (possibly intentionally, so Blue Cosmos could start another war).
The Minerva's forces successfully broke Junius Seven into two pieces just as it began entering the upper atmosphere. As the two pieces entered the atmosphere the Girty Lue and the survivors of the Joule team withdrew, but the Minerva continued to pursue the debris, breaking it into smaller fragments with her main Tannhäuser positron cannon. The destruction was still insufficient, and the remaining pieces landed on Earth, destroying Athens, Philadelphia, Quebec City, part of the Great Wall of China, Shanghai, Rome, Prague and numerous other locations, while pieces that hit the sea caused massives tsunami and tidal waves. The most severe damage occurred near the equator.
An alliance of the Junk Guild, the Serpent Tail and Rondo Mina Sahaku tried to use GENESIS Alpha to push away the remains of Junius Seven, but due to the intervention of the RGX-00 Testament Gundam the operation failed.
In the aftermath of the disaster, PLANT/ZAFT immediately sent humanitarian aid to Earth. Lord Djibril, the new leader of Blue Cosmos, took advantage of the incident and divulged photographic evidence showing the rogue ZAFT units executing the drop, and started to manipulate the public opinion into blaming coordinators for the disaster. He also used his position within the secret society LOGOS in order to influence or even directly command the leaders of the Atlantic Federation to start another war against PLANT.
The Second Alliance-PLANT War
Fueled by public opinion, manipulated by Blue Cosmos, the president of the Atlantic Federation to sent a list of demands to PLANT's supreme council. PLANT was blamed for harboring the terrorists that had committed the drop, even though all had been killed. The demands required PLANT to dismantle its military, dismiss the current PLANT Supreme Council, and to submit to Earth Alliance inspectors.
Durandal wished to find a diplomatic solution, but the Earth military had already begun deploying forces and PLANT was forced to man its defense line.
Before the expiration of the ultimatum, the Earth Alliance attacked PLANT, officially starting the Second Alliance-PLANT War.
The Battle of Aprilius One
The Earth Alliance main force launched its battleships and mobile suits against the main PLANT defense, which managed to repel the attack. Meanwhile, a separate ambush team moved to attack Aprilius One, the location of the Supreme Council. The team launched a squadron of new GAT-04 Windam units carrying nuclear missile launchers, but fortunately a scout unit located the squadron in time. Knowing that it was very likely the Earth Alliance might try to use nuclear missiles, a Nazca-class vessel was equipped with a Neutron Stampeder and stationed on standby to protect the PLANTs from this type of scenario. When the device was activated, it sent out high frequency radiation that detonated all the nuclear weapons in the ambush fleet, which was completely destroyed by their own prematurely detonating missiles. Having failed in their mission to destroy the PLANTs with a nuclear strike, the Earth Alliance forces withdrew.
As the nuclear devices detonated in proximity of the colonies, PLANT's citizens were outraged and began pushing for a retaliatory strike against all Naturals. Durandal, knowing of the possible escalation of the conflict, used the help of a Lacus Clyne look-alike idol, Meer Campbell, to calm the people.
Durandal then assigned the ZGMF-X23S Saviour Gundam to Athrun, who had re-enlisted in ZAFT. Athrun was also appointed to FAITH, a special forces unit reporting directly to Durandal, effectively given permission to use his power as his conscience dictated. He soon departed for Earth to join the Minerva and notify Talia Gladys about her own appointment to FAITH.
Operation: Spear of Twilight
Following the Earth Alliance's failed nuclear attack, ZAFT's Defense Committee drafted a series of proposals meant to strengthen ZAFT's position. Earth Alliance forces had begun surrounding ZAFT Earth bases at Gibraltar and Carpentaria, but the surprise use of the Neutron Stampeder stalled the Earth Alliance forces. ZAFT forces gathered in the atmosphere to commence a drop operation to support Gibraltar and Carpentaria, and although they met a fierce opposition from the remaining Earth Alliance forces stationed on the moon, they defeated the Earth Alliance forces that were surrounding their bases.
Orb Enters into the Earth Alliance
Declaration to Sign into the World Security Treaty Organization
Under pressure from public opinion, now fiercely against ZAFT, the Earth Alliance sought an alliance with Orb, which possessed a technically advanced and powerful military force.
The majority faction of Orb's governing body, led by Prime Minister Unato Ema Seiran and his son Yuna Roma Seiran, supported an alliance. Cagalli, Orb's representative, remained fiercely opposed. The council feared the Atlantic Federation's military strength, and wanted to avoid the events of the first war, when neutral Orb was attacked by the Earth Alliance and suffered massive casualties. Cagalli was eventually manipulated into accepting the alliance, mostly by the arguments that 'Orb cannot be burned again' and that they would be forced to withdraw the humanitarian aid they were extending to the victims of the Break the World incident.
Had Orb's original leadership not sacrificed itself during the first war, Orb may not have joined the Earth Alliance. Instead, Orb declared it would sign into the World Security Treaty Organization.
The Minerva's Ambush at Orb
Orb's council planned to give the Minerva to the Earth Alliance as a gift of good faith. The Minerva was still at dock in Orb, after the damage she took in the battle around the drop of Junius Seven.
Warned by Andrew Waltfeld, the ship departed immediately from Orb, but was ambushed by a vast Earth Alliance fleet as soon as it left Orb territorial waters. The Earth Alliance deployed the massive mobile armor YMAF-X6BD Zamza-Zah, equipped with a positron beam reflector. An Orb fleet was deployed on the border to prevent Minerva from retreating into its territory.
Despite the odds, the Minerva successfully escaped the ambush by laying waste to the opposing fleet, destroying the mobile armor and sinking several carrier ships. The new Deuterion Beam technology and Shinn Asuka's SEED factor were instrumental in the battle. The damaged Minerva headed for the ZAFT Carpentaria base in Australia.
Assassination Attempt of Lacus Clyne
After the First Alliance-PLANT War, the main figures of the Clyne Faction lived secretly at Reverend Malchio's orphanage in Orb, hiding both the Archangel as well as the stolen (and secretly repaired) ZGMF-X10A Freedom.
An unknown commando task force of Coordinators attempted to assassinate Lacus Clyne at the orphanage, but all of them were incapacitated by Freedom when they used their mobile suits to attack the bunker everyone had evacuated to. All the pilots killed themselves by self-destructing their mobile suits shortly after being defeated. The fact that the commandos were Coordinators and that they were piloting the new ZAFT aquatic unit UMF/SSO-3 ASH (then only available to elite units) suggests the team was from ZAFT. It's probable the assassination was ordered by chairman Gilbert Durandal, in order to replace Lacus with Meer Campbell.
As a result of the attack, and after the recent political events, some of the remaining Archangel crew assembled and launched the ship, departing from Orb and hiding underwater.
Kidnapping of Orb's Chief Representative
Before leaving Orb, a letter was delivered to Kira Yamato from Cagalli stating her intentions to marry Yuna Roma Seiran in support of Orb joining the Earth Alliance, along with the ring given to her by Athrun Zala. Concerned for her in her present state-of-mind and in her future with Orb, Kira launches in the Freedom from the emerging Archangel towards Orb's main island, where the wedding is taking place. There, the Freedom interrupts the ceremony by disarming all MVF-M11C Murasame and MBF-M1 Astray units present, briefly lands at the base of the altar grabbing Cagalli, and immediately takes off back towards the Archangel.
As the Freedom approaches the Archangel, the Orb Naval Patrol Ships learn of Cagalli's kidnapping by the Freedom, but since Cagalli is on the Freedom, the ships refuse to fire on the mobile suit for fear of harming her. Nevertheless, the Freedom docks with the Archangel, as the ship again submerges into the ocean: as it does, the Orb captains salute, praying for the Archangel to protect Cagalli in their place.
With the absence of Cagalli Yula Athha in Orb, Yuna Roma Seiran assumes the position of Orb's Representative and Commander-in-Chief. Orb signes the World Security Treaty, officially joining the Earth Alliance.
Skirmish on the Indian Ocean
The Battle of Gulnahan
On route to the Black Sea ZAFT base, the Minerva had to break through Earth Alliance forces stationed in the Middle East area. With the help of local guerilla units, the Minerva managed to destroy a land-based Lohengrin positron cannon fortification in the Gulnahan ravine, east of Suez. The cannon had previously been unassailable due to a Mobile Armor equipped with a positron reflector. The destruction of the fortification, which had become known as the "Lohengrin Gate", resulted in the liberation of the nearby city which had been occupied and oppressed by EA forces. The locals quickly repaid the brutality and cruelty that had been shown to them by the EA and executed numerous captured EA soldiers and officers.
The Battle of Dardanelles
On route to the Gibraltar ZAFT base, the Minerva departed from the ZAFT base in the Black Sea, but was intercepted by an Earth Alliance fleet in the Dardanelles strait. Despite the Orb Union's historical non-aggression policy, and in light of the new treaty with the Earth Alliance, Orb couldn't refuse orders from the Earth Alliance and a massive fleet comprised of several carriers containing numerous MVF-M11C Murasame mobile suit units engaged the Minerva.
Soon after, as the Minerva was about to fire its Tannhäuser positron cannon on the leading Orb ship, the cannon was destroyed by the ZGMF-X10A Freedom, piloted by Kira Yamato, killing several crewmen from the Minerva in the process. The intervention of the Archangel stalled the battle, and Cagalli tried to stop Orb officers from attacking the ZAFT forces. Her attempt failed as Jona Roma Saran declared her to be an impostor and ordered the leading Orb ship to fire on Cagalli's Strike Rouge and on the Archangel.
After Orb committed itself to the battle, the Earth Alliance fleet also joined in, contributing the three Gundam units stolen at Armory One, as well as a number of Windams. The Minerva, in response, sortied it's three remaining mobile suits, a ZGMF-1000 Zaku Warrior, a ZGMF-1001 Zaku Phantom, and the prototype ZGMF-X2000 GOUF Ignited, to back up the ZGMF-X56S Impulse Gundam and the ZGMF-X23S Saviour Gundam, both of which had already sortied to defend the ship. The fighting was fierce, with the Archangel and the Freedom trying to carefully launch attacks designed to deter combat between mobile suits and disable aggressive units. Kira quickly damages Shinn's ZGMF-X56S Impulse Gundam,and effortlessly disables or cripples Heine's ZGMF-X2000 GOUF Ignited, Stella's ZGMF-X88S Gaia Gundam, and Auel's ZGMF-X31S Abyss Gundam. However, Kira's intervention directly led to the death of Heine - In anger at Freedom's domination of the battle and at being damaged by Freedom, Heine and Stella both moved to attack Freedom and Heine unknowingly moved between Stella and Freedom - Heine and his GOUF were sliced in half by Stella on her way through.
The Earth Alliance eventually disengaged the battle after most of their mobile suits were destroyed or disabled. The Orb fleet was also forced to withdraw from the battle, mostly because of the same reason.
The Battle of Crete
The Minerva reprised its route towards Gibraltar, only to be intercepted again by the same Orb naval fleet under the orders of Colonel Todaka and Jona Roma Saran. The Archangel, with Kira's Freedom and Cagalli's Strike Rouge, unsuccessfully tried again to stop the Orb forces by disabling various units and ordering their withdrawal. The battle group under the command of Neo Roanoke also participated in the battle, closing the Minerva in a pincher move.
The Abyss and Chaos units engaged Shinn's Impulse and Athrun's Saviour respectively. Left with only two mobile suits that were limited in mobility to the ship's upper deck as cover, the Minerva was attacked by the entire Orb mobile suit force, consisting of several attack groups of Murasame units. The attack was repelled, but the Minerva took very heavy damage, including damage to both the catapults, part of the mobile suit hangar, the main deck and most of the upper armor. While defending the ship, Rey Za Burrel's ZAKU Phantom was damaged and Lunamaria's ZAKU Warrior was destroyed. Athrun's Saviour was damaged beyond repair by Kira's Freedom in a duel between the two pilots; all three pilots survived, though Lunamaria had to receive medical attention from her injuries.
While Kira was engaged with Athrun, Shinn managed to destroy the Abyss, killing its pilot Auel Neider. In supporting the Minerva, Shinn then decimated the Orb mobile suit force, and after that he directly engaged the Orb fleet, sinking several ships. The aircraft carrier Takemikazuchi launched a frontal attack on the Minerva, but under fire from the Minerva's main cannons and after a killing blow from the Impulse, it exploded and sank before reaching the Minerva. Colonel Todaka valiantly chose to go down with his ship, but he ordered his most loyal crewmembers to join the Archangel and fight for Orb's true ideals, rather than returning to the Earth Alliance.
The Destroy Crisis - The Battle of Berlin
After Lord Djibril assigned the massive mobile suit GFAS-X1 Destroy Gundam to Neo Roanoke, the designated 'Extended' human pilot Stella Loussier effectively went on a rampage and used it to completely level several cities in Western Eurasia - former Eurasian Federation territories that had sided with ZAFT - in addition to all ZAFT forces that engaged the Destroy, to show the rest of the Earth Alliance what would happen if any of them sided with ZAFT.
The Destroy was intercepted once more by ZAFT over the city of Berlin. The ZAFT units were no match for the Destroy's massive and numerous energy weapons as well as its multiple positron shields, and Berlin was heavily damaged while ZAFT forces in Berlin were utterly obliterated. Soon after, the Archangel and its complement of mobile suits (including a group of MVF-M11C Murasame's from the Takemikazuchi) arrived and commenced battle against the Destroy, much to the surprise of the ZAFT ship Minerva, which arrived shortly afterwards.
Kira Yamato in the Freedom engaged the Destroy and was later joined by Shinn Asuka in the ZGMF-X56S Impulse Gundam, while Cagalli Yula Athha in the Strike Rouge and three Orb Murasames engaged the ZGMF-X24S Chaos Gundam. Both the Minerva and the Archangel provided support to their mobile suits from the rear. When the Destroy's cockpit was cut open by Shinn, Neo Roanoke communicated that the pilot was Stella before Shinn could take down the Destroy. Shinn's feelings stopped him from finishing the Destroy, and Stella's feelings for Shinn caused her to stop fighting too. During this time the Freedom approached and Stella, who had been warned by Neo that Freedom was dangerous, panicked and prepared to fire the Destroy's chest beam cannons despite Shinn being in the way. The Minerva (also being in the Destroy's line of fire) prepared to attack the Destroy with her Tristan beam cannons, but before Stella could attack Kira stabbed the Destroy's chest beam cannons with both beam sabers to save Shinn and the Minerva, mortally wounding Stella in the process and permanently stopping the Destroy.
During the battle, Sting Oakley - the pilot of the Chaos - found himself being overwhelmed by the Archangel's Murasame units and chose to retreat, but sustained heavy damage by the trio of Murasames before he could withdraw. As his mobile suit plummeted towards the ground, it was cut in half by Murasame team leader Ikeya. The cockpit was not penetrated, but the mobile suit was critically damaged and exploded a few seconds later. Oakley was initially believed to be dead but he managed to survive and returned the Earth Alliance, after which he was transferred and stationed at Heaven's Base.
Kira Yamato, sensing something familiar in Neo Roanoke again, disabled his Windam and allowed Neo himself to be captured by the Archangel. Stella died in Shinn's arms.
At the end of the battle, Berlin was nearly destroyed, which led to increasing tension between the Atlantic and Eurasian Federations and led to the break down of the original Earth Alliance - this essentially left the Atlantic Federation to fight ZAFT on their own. And when Gilbert Durandal revealed LOGOS on international TV shortly after, Lord Djibril's plan to keep Eurasia in line with the Destroy essentially backfired, as it triggered the total collapse of the Earth Alliance and more importantly, revealed the existence of LOGOS itself as the cause of the war. Additionally all footage of the Archangel and the Freedom were omitted from ZAFT's television coverage during Durandal's speech to make it look like that only ZAFT came to aid the people of Berlin.
Campaign Against LOGOS Begins
Durandal Exposes LOGOS
After the battle, at a news conference that was broadcast across the PLANTs and Earth, Chairman Durandal told people that there was an information gap, so he showed video footage of the war and gave a speech: He says that the Alliance's excuse was to liberate Western Eurasia from ZAFT, but asked if destruction was liberation (with the Impulse gaining credit for defeating the Destroy due to the removal of the Freedom from the video footage covering the event). Meer Campbell joined the conference and says that the war was set up by ZAFT radical extremists. Durandal says that ZAFT was supporting those who wanted to break free of the Alliance for humanitarian reasons.
He reveals to the people of Earth and the PLANTs that LOGOS, the Alliance's shadowy military-industrial benefactors had been manipulating world events and were the cause of major wars, including the Alliance-PLANT Wars. He explained that even the Alliance's Blue Cosmos rulers were just a tool of LOGOS. When he showed the photos and names of all LOGOS members (including Djibril, who unsuccessfully ordered the broadcast to be cut off), Durandal said that LOGOS wanted people to fight for their profit and vowed that ZAFT would destroy LOGOS in order to bring peace between Earth and the PLANTs. The speech greatly strengthen Earth's support for ZAFT and weakened civilian support for the Alliance. The ZAFT campaign to destroy LOGOS and Blue Cosmos had begun.
The crew of the Archangel, after seeing the broadcast, decide to head back to Orb fearing it might be attacked due to the fact that Orb was affiliated with the Earth Alliance. Several Earth Alliance naval fleets defected and stationed themselves at Gibraltar shortly after the news conference.
Operation: "Angel Down"
Operation: "Angel Down" commenced when an AWACS ZAFT mobile suit picked up the Archangel on its sensors as the Archangel was on its way back to Orb. ZAFT sends the Compton-class Uhlenbeck, one of their newer model of land battleships, and it's mobile suits, a compliment of TMF/A-802 BuCUEs and AMA-953 BABIs begin to attack the Archangel. The Archangel and ZGMF-X10A Freedom Gundam tried to escape.
The goal of the operation was to sink the Archangel and destroy the Freedom, as the ZAFT HQ claimed that they had only caused confusion during the war. The Minerva was ordered to take part in the battle. If the Archangel made it to the sea and managed to dive, the battle would be over.
When the Minerva arrived, the Impulse engaged the Freedom. The Compton stopped its attacks. Impulse repeatedly blocks Freedom from defending the Archangel or running away. The Impulse's pilot, Shinn Asuka, had been studying the moves of the Freedom with help of Rey Za Burrel, and used an array of preplanned surprise tactics to battle the Freedom, allowing him to easily outperform Kira.
During the battle, Talia Gladys, Captain of the Minerva, tells the Archangel to surrender and they would be spared. Captain Ramius, Captain of the Archangel politely refuses, claiming that they only wish to return to Orb and that the ship still had things to do. At this point the land battleship resumed its attack, claiming that Gladys was too soft.
At the climax of the battle, the Archangel begins to dive into the sea, while the Minerva fires its Tannhauser positron cannon in a last ditch attempt to stop the Archangel. Once the positron beam hits the ocean, it generates a massive explosion, which heavily damages the submerged Archangel, but does not directly destroy the ship. Captain Ramius then orders one of the damaged engines to be jettisoned and detonated as a ruse to buy time for their escape. It was later confirmed by ZAFT's underwater search team that the Archangel had indeed escaped intact.
At the same time, the Impulse makes creative use of its many Silhouette packs, its ability to separate into smaller parts (and, by extension, to receive replacements for damaged parts), and by taking advantage of Kira Yamato's fighting style (which primarily involves disabling the enemy MS weapons/cameras), as well as Kira's unwillingness to kill, manages to impale the Freedom with an anti-ship sword. Kira Yamato managed to disable the Freedom's nuclear reactor in time, which, as a side effect, shut down his unit's phase shift armor, allowing his unit to be torn apart when it was hit by the shockwave of the nearby explosion (caused by the Minerva's positron blast striking the water). Shinn Asuka believed that his attack had completely obliterated the Freedom and therefore avenged Stella's death. In truth, the shielded cockpit in the upper torso survived intact, and Kira was later rescued by his sister, Cagalli Yula Athha.
Desertion of Athrun Zala and Meyrin Hawke
After Operation: "Angel Down", Athrun was angry that ZAFT had to destroy the Archangel as Kira Yamato was his friend and because he believed that their motives were to reduce the bloodshed, but Gilbert Durandal thinks that they have only caused confusion throughout the war. After he unveils the ZGMF-X42S Destiny Gundam and the ZGMF-X666S Legend Gundam, Durandal and Rey Za Burrel have a meeting and decide that Athrun's emotional attachement to the Archangel prevents him from being any more useful to their purposes, they decide to frame him as a traitor, which Meer Campbell overhears. After Meer warns him of his impending arrest, Athrun ambushes the MPs sent to arrest him.
Athrun then escapes into Meyrin Hawke's room after Meer refuses to go with him. After Meyrin sets off a false alarm to distract the soldiers, the two escape in a GOUF mobile suit. However, they were found by Rey Za Burrel during their escape, and afterwards are pursued by both Shinn and Rey in the Destiny and Legend. Despite Athrun's objections to Shinn about how he is being deceived by both Durandal and Rey, Rey convinces Shinn that Athrun is unstable and the GOUF is destroyed by Shinn's Anti-Ship Sword. However, Athrun and Meyrin were rescued by Ledonir Kisaka, the former Kusanagi captain and Cagalli's bodyguard from the first war, who was posing as an Earth Alliance officer on board one of the defecting Earth Alliance ships. The two are transferred to the Archangel's infirmary in Orb.
Meanwhile, Durandal fabricates evidence that Athrun and Meyrin were working for LOGOS, and that they accessed classified information before they left.
The Battle of Heaven's Base - Operation: Ragnarök
ZAFT and defected Earth Alliance forces mobilize for a siege of Heaven's Base, the headquarters of the LOGOS benefactors of the Earth Alliance's Blue Cosmos rulers. They give them the choice of handing over the LOGOS members and dismantling or being attacked. Before the time limit expired the ZAFT/EA forces are answered by a sudden barrage of rockets. Also, a great number of mobile suits, some new mobile armors as well as five GFAS-X1 Destroy Gundam units (one unit piloted by former ZGMF-X24S Chaos Gundam pilot Sting Oakley) are deployed against the joint ZAFT/EA forces. Because of this, many of the anti-LOGOS EA ships and mobile suits (conveniently placed near the front of the formations) are destroyed, especially by the GFAS-X1 Destroy units. Soon ZAFT forces begin suffering casualties. In response, ZAFT launches an attack from above by dropping a great number of mobile suits from Earth's orbit. However, LOGOS is well prepared for this and orders the activation of the powerful Nibelung weapon, which sends out a massive energy burst (in similar fashion as GENESIS superweapon), destroying all units coming from above and crippling the already weakened forces.
The Minerva finally launches the Destiny, Legend and Impulse (piloted by former Gunner ZAKU Warrior pilot Lunamaria Hawke) which quickly turns the tide of the battle. Then, Lunamaria leads a group of ZAKUs, BABIs, DINNs and GOUFs against the Windams, while GOOhNs, ZnOs and ASHs take out the aquatic GAT-707E Forbidden Vortex units and shoreline defenses. Shinn and Rey attack the five Destroy units in the meantime. Shinn then orders Lunamaria to switch to the Sword Silhouette and give one sword to Rey, and the three pilots then set to work eliminating the Destroys with the Destiny's Arondight and the Impulse's Excalibur anti-ship swords. In the destruction of the five Destroy units, pilot Sting Oakley is killed when Shinn drives his anti-ship sword into Sting's cockpit. In the meantime, ZAFT forces gain the upper hand when they are able to successfully penetrate the base. After Sting's Destroy unit was lost, Lord Djibril - knowing that Heaven's Base was all but lost - abandoned the other LOGOS members and fled in a submarine towards Orb. His fellows were then captured and sentenced.
The Second Flight of the Eternal
While the Battle of Heaven's Base raged on Earth, in space another set of events are taking place. DaCosta journeyed to the Mendel colony to retrieve evidence about Durandal's plans (how the Clyne Faction learned of this is unknown). While DaCosta was examining the abandoned genetics laboratory on Mendel, he discovered a research notebook which he took and returned to the Eternal (followed discreetly by a reconnaissance-type GINN). Aboard the Eternal, Lacus and Waltfield examine the journal and ponder the meaning of the "Destiny Plan" mentioned in it; however, they are interrupted by an alarm signaling that they have been discovered by ZAFT forces.
Lacus immediately orders the Eternal to launch so they can try to deliver the ZGMF-X20A Strike Freedom Gundam and ZGMF-X19A Infinite Justice Gundam to the Archangel at all costs as well as to draw ZAFT away from the Clyne Faction's hidden mobile suit factory located nearby; As they get near Earth, they are ambushed by two more ZAFT ships and multiple squadrons of ZAKU's and GOUF's. Knowing that the situation is grim, Waltfield decides to launch in his ZGMF-X88S Gaia Gundam but is gradually fighting a losing battle against the increasing number of enemy mobile suits. Back on Earth, Kira is alarmed when the Archangel receives news about the Eternal's current situation; realizing that Lacus is in dire need, Kira launches in the Strike Rouge (with an attached booster to enable it to reach space and its settings modified to those of the original Strike). Arriving on the scene, Kira is able to back up Waltfield and disables a few ZAKU's and GOUF's, but the Strike Rouge is soon overpowered by the newer models and takes heavy damage; at this point, Waltfield contacts Kira telling him to dock with the Eternal and retrieve his new unit.
After docking with the Eternal Kira receives the Strike Freedom and launches in it. He then proceeds to decimate the entire attacking mobile suit force, numbering 25 ZAKUs and GOUFs in total, within 2 minutes. After disabling the mobile suits, Kira disables the weapons and engines on the ZAFT ships chasing the Eternal.
ZAFT's Invasion of Orb - Operation: Fury
ZAFT intelligence tracks down Blue Cosmos leader Lord Djibril to Orb, where he is being sheltered by the Seirans. Carpentaria forces gather for an invasion along with the Minerva. Chairman Gilbert Durandal issues an ultimatum demanding that Orb hands over Djibril before he escapes and unites with the remaining LOGOS benefactors at the Moon via Orb's mass driver. Yuna Roma Seiran responds to the ultimatum with an obvious lie: Djibril is not being protected by Orb and that the presence of ZAFT's fleet is an insult to the nation's sovereignty. The blatant disregard of the ultimatum enrages ZAFT leaders and Durandal authorizes the invasion of Orb to begin.
The ZAFT fleet deploys forces in the air and underwater and quickly disposes the hastily deployed Orb fleet, as the Seirans had chosen not to mobilize the military even in the face of invasion from ZAFT forces, while ground forces begin drilling into Onogoro. On the Archangel, Cagalli Yula Athha is enraged by Seiran's announcement, foreseeing it as a clear signal for Orb to burn once more (especially since the civilian population has not been made aware of the situation) and receives her father's will, the ORB-01 Akatsuki Gundam, from Morgenroete Chief Engineer Erica Simmons and Colonel Ledonir Kisaka.
After launching in the Akatsuki with the forces from the Takemikazuchi, Yuna, who is clearly fighting a losing battle against the ZAFT forces, is removed from command after Cagalli tricks him into acknowledging her as Orb's military commander (since the last time Cagalli intervened in a battle involving Orb forces, Jona labels her an impostor) and then ordering his arrest on the charge of treason. After assuming command of the Orb fleet, she successfully rallies her remaining forces and Orb begins to push back ZAFT on all fronts. However, she then confronts and is almost killed by Shinn Asuka in the ZGMF-X42S Destiny Gundam. Kira Yamato, at that moment, returns from space piloting the ZGMF-X20A Strike Freedom Gundam and after saving Cagalli, engages Shinn (who is shocked to find out that the Freedom's pilot is alive). Lacus Clyne, who returned with Kira riding the ZGMF-X19A Infinite Justice Gundam unit, lands on the Archangel to deliver the unit to Athrun Zala. While the Archangel engages the Minerva, Cagalli retreats to Orb's military headquarters. With neither pilot gaining an upper hand, Shinn and Kira's battle ends when Rey Za Burrel orders Shinn to retreat to recharge the Destiny's battery.
Athrun, after talking to Lacus and overcoming some initial reluctance, launches in the Infinite Justice to aid Kira and confront Shinn despite still being injured. Djibril begins his escape from Orb as the three ZGMF-XX09T DOM Trooper units from the covert organization Terminal arrive to join the battle. At Orb's National Military Defence HQ, an enraged Cagalli demands that a battered and literally beaten Jona tell her where Djibril is, who admits he has no idea where he is now. A resupplied Destiny launches again, this time with Rey in the ZGMF-X666S Legend Gundam. The pair prove to be a match for the new and improved Freedom, as the Strike Freedom is knocked into a moment of vulnerability. Shinn was about to use this chance for a finishing blow but is interrupted by Athrun, who rams the Infinite Justice into the Destiny and stops Shinn from destroying the Freedom. While the Freedom fights the Legend, Athrun attempts to reason with Shinn (who receives a second shock upon realizing Athrun is alive) and fights the Destiny. The Archangel then submerges underwater and turns the tide of the battle by destroying several submarines and surface ships, including Operation Fury's flagship St. Helens.
In the confusion of the battle, Djibril manages to launch in the Sarans' private shuttle. The Orb fleet sends Murasames in pursuit while the Minerva's Commanding Officer Talia Gladys orders Lunamaria Hawke to shoot down the shuttle in the ZGMF-X56S Impulse Gundam. When the shuttle manages to escape into space despite Orb and ZAFT sending units after it, Gladys orders a retreat and ZAFT forces disengage from the battle. Athrun collapses as the ZAFT forces withdraw and is rushed back to the Archangel by Kira for emergency medical treatment.
While there was no official confirmation that Djibril had indeed escaped, Durandal agreed with Talia's decision. Post-battle, Cagalli addresses the world regarding the ZAFT invasion, but she is interrupted by a broadcast by Meer Campbell (again posing as Lacus Clyne), to turn public opinion against Orb for sheltering Djibril. In response, the real Lacus Clyne interrupts Meer's broadcast, introducing herself as the real Lacus and declares that she still supports the Archangel. She goes on to say that she does not approve the actions of Chairman Durandal nor of Lord Djibril, and that people in the world should stop blaming everyone but themselves for the war.
The Requiem Tragedy - Djibril's Attack on Aprilius One
After Lord Djibril's escape, he makes it to the new Daedalus lunar base on the dark side of the Moon and authorizes the activation of the Requiem superweapon. The Requiem consists of an emormous beam cannon site on the moon and several orbital relay stations built from abandoned colonies that use oversized Geschmeidig Panzer systems to change the course of the beam. Fired from the fixed moon site, the beam is then bent at each relay point, and eventually guided to the primary target in this manner. Djibril orders it to be fired at PLANT's capital, Aprilius One, in order to eliminate PLANT's Supreme Council and Durandal, not knowing that he was on Earth. However, due to combat at the last relay station between the EA escort fleet and the Joule squad of ZAFT, the beam goes slightly out of alignment and instead hits Januarius 1 to 4, with Januarius 4 colliding into December 7 and 8 in its destruction, killing an estimated 900,000 Coordinators. The Joule team destroys the damaged relay station in retaliation, but after recharging there are still multiple relay stations remaining that Requiem could still use to fire again at the PLANTs.
At around the same time, from the notes on Chairman Durandal's Destiny Plan, the crew of the Archangel discover what his true intention is: Durandal plans to implement a new world order where every human is given the role for which they are best genetically suited for at birth, to fulfill his ideal of perfect genetic determinism. So the crew of the Archangel decides to head to space in order to stop Durandal's plan from succeeding.
The Battle of Daedalus
While Lord Djibril waits for the Requiem to be recharged for another attempt at destroying Aprilius One, Chairman Durandal orders the ZAFT Moon Fleet to attack the relay stations in retaliation for the Requiem attack, ZAFT forces (including the Joule Squad) attacked furiously but were at a stalemate with the defending EA forces. The Minerva along with the Rey Za Burrel's Legend and Shinn Asuka's Destiny Gundams, launch a surprise attack on the Daedalus lunar base as a diversionary tactic to allow Lunamaria Hawke in the Impulse Gundam to infiltrate the base and access Requiem's firing chamber through a connecting service tunnel. The EAF scrambles all its fixed defenses, its last three GFAS-X1 Destroy Gundams, several mobile armors and countless GAT-04 Windams to defend the base.
At the Fourier relay station, ZAFT managed to knock it out of position before Requiem is fully recharged, but Djibril orders that Requiem be fired anyway to wipe out the ZAFT forces there, and so he can use it as a cover to escape to the Arzachel lunar base in the Girty Lue.
However, Lunamaria succeeds in destroying the Requiem control centre before it can fire, and the Minerva along with Shinn's and Rey's units destroy the base's defenses. Shinn destroys the base's hangar and command centre, while Rey detects the launch of the Girty Lue and destroys it, killing Lord Djibril (the last member of LOGOS and Blue Cosmos leader). The defending Earth Alliance forces then surrender, and seem to be treated well by the ZAFT forces.
The "Destiny Plan"
Second Assassination Attempt in Copernicus City
When the Archangel and its crew reaches space, it docks at the free city of Copernicus on the moon, where Kira Yamato, Athrun Zala, Lacus Clyne, and Meyrin Hawke go for a shopping trip to the city. After being sighted, ZAFT bodyguards assigned to protecting Meer Campbell set a trap with the objective of eliminating Lacus Clyne. Using Meer's Haro, they send a note to Lacus and company indicating that Meer is about to be killed. Although they suspect it to be a trap, Athrun insists on trying to find her anyway, and Lacus states she wishes to see Meer as well. They meet with Meer, who becomes surprised and enraged to see the real Lacus. After trying to shoot Lacus with a pistol, however, Meer comes to her senses and comes to accept that she is not Lacus Clyne. Their meeting is short-lived, however, as Sara, leader of the ZAFT bodyguards, attempts to eliminate Lacus by summoning a squad of ZAFT bodyguards to gun down the group. Athrun manages to kill the bodyguards, and Sara (or so he thought). Sara manages to get off another shot at Lacus before Kira and Athrun can react, but Meer - in an attempt to shield Lacus from harm - is shot instead. Kira and Athrun then fire back at Sara, killing her. Kira calls for Neo Roanoke in the ORB-01 Akatsuki Gundam to take them back to the Archangel for Meer to receive medical treatment, but Meer dies before she can be moved.
Durandal Reveals the "Destiny Plan"
Almost immediately after the assassination attempt in Copernicus City, PLANT chairman Gilbert Durandal appears in a global broadcast, taken aboard the ZAFT space mobile fortress Messiah. From the Messiah, he address the Requiem attack on PLANT, and assures the world that LOGOS has been defeated. However, he announces that there is one more enemy that humanity has to face, an enemy he addresses as "ignorance and ambition". He accuses Naturals of being too self-centered and conceited, essentially causing the suffering of others. Thus, he then announces that he has the solution to this problem, and reveals the "Destiny Plan" - every human and Coordinator will be assigned the role that they are the most genetically suited to.
The Atlantic Federation is the first to decide not to follow the plan, and the Arzachel Lunar Base mobilizes its remaining forces in defense while the president of the Atlantic Federation (who is at Arzachel Base) attempts to contact chairman Durandal. Without even responding to the request for contact, Durandal uses the captured and repaired Requiem superweapon to destroy the Arzachel Lunar Base, destroying the base, part of the Alliance fleet and killing the president as well.
Subsequently, the Orb Union and the Kingdom of Scandinavia are the only other nations left to reject the Destiny Plan, and soon Orb and Terminal (the organization that the Three Ships Alliance grew into between the wars), understanding the message sent by Chairman Durandal through the destruction of Arzachel Base with the Requiem, mobilize their military forces to destroy Requiem.
The Orb Union launches its space fleet from the lunar free city of Copernicus, consisting of the Archangel, the Izumo class battleship Kusanagi and two other Izumo class battleships). Lacus Clyne's flagship, the Eternal, leads a number of Earth Alliance and ZAFT battleships loyal to Terminal: and Earth Alliance ships that survived the Requiem attack on Arzachel. Their Earth Alliance forces consisted of at least two Agamemnon-classs, at least two Nelson class battleships and four or more Drake class escort ships, and their ZAFT forces consisted of two or more Nazca-classs and two Laurasia-class frigates.
Attack on Requiem and Station One
As the Archangel and Eternal approach Requiem's first relay station (Station One), they encounter ZAFT's defense forces guarding the station. Lacus Clyne attempted to convince the defending ZAFT forces to stand down but fails. As a result, an intense battle brokes out between Terminal and ZAFT.
During the battle, Terminal laid waste to the ZAFT forces at Station One and took out countless numbers of mobile suits and ships before ZAFT's Lunar fleet, led by the Minerva, joined the battle and slowed Terminal's progress. In a battle between the Archangel and the Minerva, Neo Roanoke regained his memories as Mu La Flaga after blocking a positron blast from the Minerva with his mobile suit (ironically almost exactly how Flaga had blocked a similar blast in the first war and led to his memory loss) and inflicted considerable damage to the Minerva by destroying its positron cannon shortly afterwards. In the closing stages of the battle, Yzak Joule and Dearka Elsman (piloting a custom-coloured ZGMF-2000 GOUF Ignited and a ZGMF-1001/M Blaze ZAKU Phantom respectively) revealed themselves to be members of Terminal and switch sides, protecting Kira Yamato and Athrun Zala (in the ZGMF-X20A Strike Freedom Gundam and ZGMF-X19A Infinite Justice Gundam respectively) while they use their METEOR unit's heavy beam swords to slice Station One in two.
In the mean time, the combined Terminal/Orb fleet attacks Requiem's main cannon, with much less success. Although the three leading Orb Izumo class ships fire their twin Lohengrin positron cannons at the Requiem, they were unable to penetrate Requiem's positron reflectors. Without warning, ZAFT's mobile fortress Messiah appeared from behind the moon and fires its Neo-GENESIS superweapon, resulting in the destruction of part of the combined fleet. The battle immediately following the Neo-GENESIS attack would become known as the Battle of the Messiah.
The Battle of The Messiah
The Archangel, Eternal and the rest of the Terminal fleet regrouped with the Orb fleet and began engaging the ZAFT forces defending the Messiah space fortress and the Requiem. However, with Requiem's second station moving closer into firing position to destroy Orb, Kira Yamato, pilot of ZGMF-X20A Strike Freedom Gundam, told the Archangel and Athrun Zala, pilot of ZGMF-X19A Infinite Justice Gundam, to leave the Eternal and break through the Requiem's defenses and destroy it while he and the Eternal attack the Messiah. The defensive hole this left at the Eternal was filled in by Yzak Joule in his ZGMF-2000 GOUF Ignited and Dearka Elsman in his ZGMF-1001/M Blaze ZAKU Phantom.
On the way to the Messiah, Kira was engaged by the ZGMF-X666S Legend Gundam, piloted by Rey Za Burrel, who blamed Kira for his flawed existence. However, Rey was shaken up by Kira's reasoning as to his own life, and the Legend was nearly destroyed when Kira fired all the Freedom's weapons at the Legend, with almost every shot connecting. In the meantime, Athrun was attacked by Lunamaria Hawke piloting the ZGMF-X56S Impulse Gundam, Athrun easily disabled the Impulse, but was attacked by the ZGMF-X42S Destiny Gundam, piloted by Shinn Asuka. Lunamaria eventually tried to put herself between the two to stop the fight, but when Shinn (still unable to overcome his blind rage while in SEED mode) came close to destroying the Impulse to get to Athrun. Athrun saved Lunamaria in time by totally disabling Destiny in two attacks, sending it crashing to the moons. Lunamaria went after Shinn.
Shortly after this, the Minerva, which had engaged the Archangel, was severely damaged when the Archangel destroyed both its beam cannon turrets, missile launchers, and mobile suit launchers while Athrun disabled its engines soon afterwards. The Minerva crash-landed on the Moon, a wreck, but the crew survived. Meanwhile, ZAFT Chairman Gilbert Durandal authorized the firing of the Requiem and ordered the Neo-GENESIS to fire on the Orb fleet. However, as he informed his forces of the Neo-GENESIS firing, Yzak Joule tipped off the Eternal and told them to move their fleet out of the way. Thus, the Neo-GENESIS missed its target, destroying some of Terminal's Earth Alliance ships and some of the loyal ZAFT vessels pursuing them. As the Requiem prepared to fire to destroy Orb, the Infinite Justice and the ORB-01 Akatsuki Gundam managed to penetrate the Requiem's positron reflector shields and destroy the Requiem's power core (at the cost of Infinite Justice's backpack/subflight lifter.
The Strike Freedom (using one of the METEOR units) and the Eternal managed to destroy the Messiah's Neo GENESIS superweapon with a mass missile attack at about the same time the Requiem was destroyed. Kira then broke through Messiah's beam shields and heavily damaged the structure, and then infiltrated the Messiah in order to assassinate Durandal. Rey and Talia Gladys, captain of the Minerva, also infiltrated the Messiah to seek Durandal.
As Kira and Durandal come to a tense philosophical standoff, with pistols drawn by all, Rey, completely shaken by Kira's words (which challenged everything he had been raised to believe about his purpose in life), shoots Durandal in an act of frustration. As a clone, Rey had a shortened lifespan and was raised to believe that his only purpose in his short life was to help Durandal implement the Destiny Plan, the only way to end all wars. Hearing Kira's words and realising that the Destiny Plan would rob all of humanity of the very thing he was denied (a future of his own), he realized the Destiny Plan was too high a price to end war.
Both Rey and Gladys choose to stay on board the Messiah to accompany Durandal to his death, and they died along with Durandal as the Messiah explodes. Kira was able to escape the Messiah before it crashed on the Moon.
In the "Final Plus" episode (the extended version of the last episode), Athrun also entered the Messiah and was responsible for identifying Gladys, instead of Kira alone as shown in the original version (i.e. in FINAL-PHASE). He escaped in the ZGMF-X19A Infinite Justice Gundam, along with Kira in the ZGMF-X20A Strike Freedom Gundam, and later Athrun rescued Shinn and Lunamaria from the surface of the moon.
Sometime in CE 74, PLANT and Orb Union signed a ceasefire agreement and started negotiating for an end to the war. The PLANT's Supreme Council later requested Lacus Clyne, who had acted as a mediator between the two nations, to return. Lacus eventually becomes the chairwoman of the PLANT Supreme Council.