- Phase 01 - False Peace
- The Orb Space colony of Heliopolis is attacked by ZAFT, despite its neutrality in the 11 month war. A young Coordinator, Kira Yamato, accidentally sees the Earth Alliance's new mobile weapons, which have been secretly constructed at Heliopolis' Morgenröte factory, and encounters his childhood friend, Athrun Zala, now one of the enemy.
- Phase 02 - Its Name: Gundam (It's Name is Gundam)
- Kira Yamato reprograms the Strike and defends Heliopolis. Ensign Natarle Badgiruel takes command of the new mobile assault ship Archangel with the surviving crew members.
- Phase 03 - Collapsing Land
- Mobile armor pilot Lt. Mu La Flaga joins the crew of the Archangel after his transport is destroyed. Heliopolis is destroyed. Lt. Murrue Ramius takes over as Captain of the Archangel while Ensign Natarle Badgiruel remains as XO and combat commander.
- Phase 04 - Silent Run
- The Archangel tries to elude Rau Le Creuset and head for the Eurasian Union military satellite Artemis.
- Phase 05- Phase Shift Down
- Mu La Flaga and Kira Yamato launch a counter offensive against ZAFT ship Vesalius. The Strike's phase-shift armor runs out of power in the middle of a battle with the Rau Le Creuset Team.
- Phase 06 - The Vanishing Gundam
- The Archangel and its crew are held captive by the Artemis. The Blitz Gundam attacks Artemis, using its mirage colloid armor to remain effectively invisible. Kira gets taunted for being a traitor.
- Phase 07 - The Scar of Space
- The Archangel forages for supplies in the Debris Belt. The horrors of Junius 7 are witnessed.
- Phase 08 - The Songstress of The Enemy Forces
- Lacus Clyne, the daughter of PLANT Supreme Council Chairman Siegal Clyne, is brought aboard the Archangel, causing tension within the crew.
- Phase 09 - The Fading Light
- The Archangel's escort to meet with the 8th fleet is attacked by the LeCreuset team. Flay witnesses the death of the father when Kira fails to protect the escort ships due to his inability to kill Athrun. In desperation, the Archangel reveals Lacus is on board the ship.
- Phase 10 - Crossroads
- Kira returns Lacus to Athrun, but steadfastly refuses to leave the Archangel because he wishes to protect his friends.
- Phase 11 - The Awakening Sword
- Kira's desire to fight to protect his friends on board the Archangel awakens an unknown almost berserker ability to defeat the attacking Duel, Buster, and Blitz Gundams.
- Phase 12 - Flay's Decision
- After overcoming the initial shock of her father's death, Flay decides to enlist in the Earth Alliance, prompting Tolle, Miriallia, Kuzzy, and Sai to do the same. Kira finds himself staying on board the Archangel as well in order to continue protecting his friends.
- Phase 13 - Stars Falling in Space
- The Archangel descends to Earth, but not without the loss of the entire 8th Fleet and separating the members of the LeCreuset team, with Yzak and Dearka on Earth and Athrun and Nicol still in space.
- Phase 14 - Within Endless Time
- Recap episode. Also explains the creation of Coordinators, especially the first, George Glenn.
- Phase 15 - The Respective Solitudes
- The Archangel lands in the Sahara in northern Africa, which is ZAFT controlled territory and way off their intended target, Alaska.
- Phase 16 - Burning Sandstorm
- Kira must fight off ZAFT forces in the desert, his first battle on Earth. His ability to adapt amazes the deadly Andrew Waltfeld, ZAFT's Desert Tiger. The battle ends with rebels coming to the aid of Strike and the Archangel.
- Phase 17 - Cagalli Returns
- Kira is reunited with Cagalli, the mysterious young woman he first encountered at Heliopolis' Morganroete factory.
- Phase 18 - Payback
- Though the infamous Desert Tiger has spared the lives of innocent civilians, Desert Dawn members brashly go to challenge the ZAFT forces for the devastation caused. The attack ends in failure, but most are saved by the timely interference of Kira.
- Phase 19 - Fangs of the Enemy
- Kira and Cagalli are sent into a nearby ZAFT controlled town to gather supplies with Natarle and Desert Dawn. The two teenagers unwittingly encounter the surprisingly insightful Desert Tiger, Andrew Waltfeld.
- Phase 20 - On a Calm Day
- Athrun and Nicol are given the day off to spend with their families; Athrun spends the day with Lacus and they talk of Kira. The PLANT Supreme Council debates on whether or not Operation Spitbreak should be executed.
- Phase 21 - Beyond the Clouds of Sand
- Kira and the Desert Tiger fight a battle where one of them must die, a more than painful battle for both combatants as they realize the pain of having an enemy who is not an abstraction.
- Phase 22 - The Sea Dyed Red
- The Archangel crew is clear to cross the Red Sea and head towards the neutral Orb Union with Cagalli and Kisaka tagging along. With the previous battle weighing heavily on him, Kira talks to Cagalli about his reasons for fighting.
- Phase 23 - Fateful Encounter
- A battle between ZAFT submarine forces led by Commander Marco Morrassim prevents Kira from fighting alongside Mu and Cagalli in their Skygraspers. The navigation system on Cagalli's Skygrasper goes out and she is shot down; but not before shooting down Athrun's transport. He is ejected from the transport and is stranded on the same island with her.
- Phase 24 - War for Two
- Cagalli and Athrun find themselves stranded on a deserted island together while waiting for rescue. Cagalli shoots Athrun in the arm. The two come to realize fighting may be the only way to end the war and bring about peace.
- Phase 25 - The Land of Peace
- The Archangel enters the neutral nation of Orb under the pretence the ship has been chased away. Athrun, now in charge of the members of the Le Creuset Team, sneaks into the nation with the belief the Orb's official statement is false.
- Phase 26 - Moment
- A clip show, recapping the first 25 episodes. Narrated by T.M. Revolution as Miguel Aiman (in the English dub, by Tony Sampson, Miguel's voice actor).
- Phase 27 - Endless Rondo
- Another clip show, mostly featuring Chief Engineer Erica Simmons of Morganroete and her theories on the "SEED" (Superior Evolutionary Element Destined) factor. She works with Kira to develop a mobile suit operating system that can be used by Naturals.
- Phase 28 - Kira
- Lord Uzumi and Kira's parents meet and hint there they may be a deeper connection than expected between Kira and Cagalli. Kira and Athrun meet in the most unlikely of places, perhaps for the last time.
- Phase 29 - The Turning Point
- The Archangel leaves Orb territory for Alaska and the Zala team engage them in a battle. Kira moves to kill Athrun but Nicol makes the ultimate sacrifice for his friend...
- Phase 30 - Flashing Blades
- The Zala team make their last effort to destroy the Archangel and the Strike. Dearka is shot down by Mu and forced to surrender. Tolle, Cagalli's replacement as a mobile armor pilot, makes the mistake of trying to interrupt Kira and Athrun's deadly duel. The grief the two friends suffer is enough for them to kill each other...
- Phase 31 - Grieving Skies
- The crew of the Archangel grieve for the apparent deaths of Kira and Tolle. Cagalli goes to find Kira but instead finds Athrun and confronts him for killing Kira. Meanwhile, some children and a man have found an injured young man in front of their house.
- Phase 32 - In the Promised Land
- The Archangel finally arrives in Alaska. A grief-striken Miriallia attacks Dearka, now a prisoner on board the Archangel, but ends up saving his life when Flay tries to shoot him. Kira awakes and finds himself in the care of Lacus Clyne.
- Phase 33 - Gathering Darkness
- The crew of the Archangel find themselves under inquisition for their actions regarding their escape from Heliopolis, the fall of the 8th Fleet, and entrusting the Strike Gundam to Kira Yamato. Meanwhile, Lacus comforts Kira, who is questioning his right to live and for trying to kill Athrun.
- Phase 34 - Seen and Unseen
- Natarle, Mu, and Flay are all to be transfered off the Archangel. Mu suspects that something is not quite right as the Alaska base is evacuted and Flay follows him. First appearance of the ZGMF-X10A Freedom. Lacus and her father decide to entrust Kira with the Freedom Gundam, equipped with Neutron Jammer Cancellor technology.
- Phase 35 - The Descending Sword
- Operation Spitbreak is initiated, with both ZAFT and the Earth Alliance believing they have outsmarted the other. The Archangel is left behind to be destroyed in a cruel and calculating plan that would decimate everyone on the battlefield until a familiar face arrives to save them all.
- Phase 36 - In the Name of Justice
- First appearance of the ZGMF-X09A Justice. Lacus, now denounced a traitor to the PLANTS for handing the Freedom over to an unknown pilot, confronts Athrun and challenges him to decide what he truly is fighting for.
- Phase 37 - Divine Thunder
- Kira and the Archangel make their way to Orb, where Lord Uzumi welcomes them and asks that they decide for themselves why are they fighting. The Panama Mass Driver is destroyed by ZAFT in retaliation for the blow they took at Alaska. Chief Engineer Erica Simmons presents a reconstructed Strike Gundam for the Archangel crew's use.
- Phase 38 - Decisive Fire
- Murrue decides the Archangel will support Orb in whatever decision it makes; crew members are discharged if they wish to join the Orb civilians if they no longer wish to fight. Muruta Azrael, leader of Blue Cosmos, attacks Orb with three new machines with equally deadly pilots in order to force the nation to concede to the Earth Alliance.
- Phase 39 - Athrun
- Athrun must make a decision regarding whether he should continue obeying his father's orders or fight for what he believes in.
- Phase 40 - Into the Dawn Skies
- The Archangel and the Orb ship Kusanagi launch into outer space, while the leaders of Orb stay behind. They destroy Orb's mass-driver and armaments factories, sacrificing their own lives in the process.
- Phase 41 - Trembling World
- Cagalli, though grief striken with her father's death, confronts Kira with a mysterious photograph, given to her by Lord Uzumi, of a woman with two infants and Kira and Cagalli's names written on the back. Athrun decides he must have one last opportunity to speak with his father.
- Phase 42 - Lacus Strikes
- Lacus Clyne and Andrew Waltfeld join forces, stealing the ZAFT support ship, Eternal, and rescue Athrun Zala. They join forces with the Archangel and the Kusanagi.
- Phase 43 - What Stands in the Way
- The newly-formed "Three Ship Alliance" takes shelter at the abandoned Mendel Colony. Unfortunately, they are tracked there by both Rau Le Creuset's team and Capt. Natarle Bagiruel, commanding the Dominion, the second ship of the Archangel-class.
- Phase 44 - Helix Encounters
- Mu and Dearka enter the Mendel colony to confront Rau Le Creuset and Yzak. Kira comes to aid them and he and Mu are shocked to discover Rau has more than a few secrets to reveal.
- Phase 45 - The Opening Door
- Kira and Mu are faced with terrifying revelations in an encounter with Rau Le Creuset. Dearka and Yzak have their own fateful meeting where they question as to what they are truly fighting against.
- Phase 46 - A Place For the Soul (Where the Soul Belongs)
- Flay Allster is rescued by the Dominion, and gives Muruta Azrael the disk she was given by Rau Le Creuset. It contains the specs on the Freedom and Justice Gundams, including their N-Jammer Cancellers.
- Phase 47 - The Nightmare Reborn
- Equipped with N-Jammer Cancellers, the Earth Forces launch an all-out attack on the PLANTs. The Boaz military asteroid is destroyed by nuclear weapons.
- Phase 48 - Day of Wrath
- ZAFT chairman Patrick Zala strikes back at the Earth Forces with G.E.N.E.S.I.S. (Gamma Emission by Nuclear Explosion Stimulate Inducing System): a huge gamma-ray laser. The Earth forces are forced to withdraw, but only temporarily.
- Phase 49 - The Final Light
- G.E.N.E.S.I.S. cripples the Earth Forces' reinforcements, then destroys their lunar base. Rau Le Creuset sorties in his new Providence Gundam. Mu La Flaga apparently dies protecting the Archangel (although the Special Edition omits evidence of his demise, paving the way for his return in Destiny). Muruta Azrael and Natarle Badgiruel go down with their ship.
- Phase 50 - To A Future That Never Ends (Towards an Endless Tomorrow)
- The Archangel, Kusanagi and Eternal plunge headlong into the battle, trying to keep either side from using their weapons of mass destruction. Rau Le Creuset destroys Fllay Allster's escape shuttle, killing everyone on board. Kira destroys him with the Freedom, while Athrun remote-destructs the Justice and destroys G.E.N.E.S.I.S. With both the PLANTS and the Earth Forces in disarray, the renegades moderate faction of the PLANTS seize the opportunity to force a cease-fire, effectively ending the war.
- After Phase - In the Valley of Stars (OVA)
- The war has ended, and at Malchio's orphanage in the Marshall Islands, Kira, Athrun, Lacus and Cagalli reflect on the past and discuss what the future will hold.
Gundam SEED Special Edition
- Special I - The Empty Battlefield
- Covers the events of Gundam Seed Phases 1-21
- Special II - The Distant Dawn
- Covers the events of Gundam Seed Phases 22-40
- Special III - The Rumbling Universe
- Covers the events of Gundam Seed Phases 41-50
Gundam SEED Astray
- Mobile Suit Gundam SEED ASTRAY - Volume 1-3
- Mobile Suit Gundam SEED ASTRAY R - Volume 1-4
- Mobile Suit Gundam SEED ASTRAY B - Magazine "Photonovels"
- Mobile Suit Gundam SEED X ASTRAY - Volume 1-3
Gundam SEED Destiny Astray
- Mobile Suit Gundam SEED Destiny ASTRAY - Volume 1-4.
Gundam SEED Destiny
- Phase 01 - Enraged Eyes
Two years after the first Bloody Valentine War, Cagalli and "Alex Dino" (Athrun Zala pretending as Cagalli's bodyguard) meet PLANT Chairman Gilbert Durandal to discuss important matters. At the same time, three unknown individuals infiltrate the new PLANT Armory One and steal three new next-generation ZAFT mobile suits. They are however, confronted by elite pilot Shinn Asuka in the ZGMF-X56S Impulse.
- Phase 02 - Those Who Cry Out For Battle
The battle at Armory One continues. Athrun helps Shinn in a ZAKU but fail to harm the three prototypes. Meanwhile, a Mirage Colloid cloaked ship attacks the colony, commanded by a mysterious masked man who pilots a new mobile armor.
- Phase 03 - Sign of Gunfire
- (Due to the 2004 Chuetsu Earthquake broadcast was interrupted)
The new ZAFT battleship Minerva chases the Girty Lue. Meanwhile, Cagalli and Athrun are led through the ship by Durandal but when Cagalli holds a speech about power and then she is confronted by an angry Shinn. Then they find the enemy ship and the Minerva's mobile suits are ordered to launch.
- Phase 04 - Battlefield Of Stardust
While the Minerva battles the Girty Lue, the Minerva pilots fight against the stolen ZAFT prototypes in the Debris Belt. Although at first it looks bad for the ZAFT forces, but they are able to overwhelm the enemy thanks to Athrun's plan.
- Phase 05 - Unhealable Scar
ZAFT soldiers loyal to Patrick Zala set Junius Seven on a crash course for Earth. Tensions also rise between Cagalli and Shinn due to Shinn blaming the Athha family for his family's death. Meanwhile, Lord Djibril and Logos bigwigs decide to use the Junius Seven incident to destroy the PLANTs. While Yzak Joule and his squad plan to destroy Junius Seven's debris, they are confronted by GINN High Maneuver II units.
- Phase 06 - When The World Ends
A three way battle between ZAFT, the Phantom Pain and the GINN High Maneuver II types takes place at the debris of Junius Seven while it moves towards Earth. Athrun also helps in a ZAKU but is confronted with memories of his father when it turns out that the terrorists still believe in the path that Patrick Zala had chosen. Despite the tries of the Joule team and the Minerva crew, Junius Seven continues to move towards Earth.
- Phase 07 - The Dazed Earth
The Minerva uses it's Tannhauser cannon to destroy the large debris but hundreds of small pieces descend towards Earth and destroy cities while causing heavy damage and numerous casualties. Meanwhile, Shinn saves Athrun and they both land safely on the Minerva, which entered the atmosphere. After the incident ZAFT provides help to the damaged Earth, while the Minerva crew is informed about what the terrorists said. The Minerva then heads towards Orb.
- Phase 08 - Junction
The Minerva enters Orb where the ship is repaired and Talia meets with Maria Bernes AKA Murrue Ramius. Meanwhile, the Orb government considers an alliance with the Earth Alliance much to Cagalli's protest. Athrun meets up with Kira and Lacus and discusses with Kira what he witnessed in space and afterwards plans to go to PLANT. Shinn in the meantime visits a memorial at Orb and meets none other than Kira and Lacus.
- Phase 09 - Prideful Fangs
The Earth Alliance blames PLANT for the fall of Junius Seven and orders PLANT to disarm while they secretly prepare for an attack, in response PLANT prepares for their defense. Finally a battle starts between the two forces which almost ends in the destruction of Aprilius One when the EA uses their new GAT-04 Windams armed with nuclear weapons. However thanks to a new weapon, the attack is thwarted. Meanwhile, Athrun meets Gilbert Durandal.
- Phase 10 - Curse of A Father
Athrun talks with Gilbert Durandal about the attack on PLANT and what will happen now. Because the people at PLANT are outraged, a Lacus look-alike hired by Gilbert Durandal calms the people. Athrun finally decides to do something and Durandal shows him the new ZGMF-X23S Saviour and offers him to become it's pilot. Afterwards Athrun meets the fake Lacus again, Meer Campbell.
- Phase 11 - The Chosen Road
Cagalli tries to prevent her country from joining the Earth Alliance but the Orb council, especially the Seiran family, is against her wish to stay neutral. In PLANT, Athrun meets up with Yzak and Dearka and remembers the past while ZAFT prepares to send troops to Earth. In the end, the Minerva is warned by Andrew Waltfeld that they should leave Orb because the country will ally itself with the Earth Alliance soon.
- Phase 12 - The Sea Dyed with Blood
The Minerva leaves Orb but an Earth Alliance fleet awaits them right outside their waters. The ship is forced to break through them since Orb won't let them return. When the Alliance uses a new prototype mobile armor which can even withstand a positron blast and the situation worsens, but thanks to Shinn's SEED factor, he fights like a berserker which causes heavy damage to the Earth Alliance fleet, and ultimately, their retreat. Meanwhile, Athrun rejoins ZAFT.
- Phase 13 - Revived Wing
While the Minerva crew praises Shinn for his incredible fight, Orb joins the Alliance much to Cagalli's dislike. Meanwhile, Kira and his friends are attacked by Coordinators who try to assassinate Lacus. When they use the new UMF/SSO-3 ASH mobile suits, Kira is forced to reactivate the Freedom to protect his friends. Although he disables all the enemy suits the assassins then self-destructs all of their suits.
- Phase 14 - Departure Towards Tomorrow
Kira and friends discuss matters about PLANT during the aftermath of the assassination. During that time, they are informed that Cagalli will be married to Yuna Roma Seiran. Kira decides to use the Freedom to abduct Cagalli from the ceremony, returning to the Archangel. Yuna orders Cagalli's immediate capture. Instead, Colonel Todaka salutes while letting the Archangel submerge into the ocean.
- Phase 15 - Return to the Battlefield
Athrun is reinstated to the ZAFT military and appointed to FAITH. He is given the Saviour mobile suit and assigned to the Minerva. Captain Gladis is also appointed to FAITH, which creates something of a conflict in the command structure; Athrun and herself now have more or less equal rank and strategic authority.
- Special Episode - Mobile Suit Gundam Seed Destiny -EDITED- (Recap)
A recap of the last 15 episodes which informs about the political situation in the Earth sphere.
- Phase 16 - The Battle in the Indian Ocean
As the Minerva leaves Carpentaria it is once again attack by Phantom Pain. A furious fight ignites between the two sides.
- Phase 17 - A Soldier's Qualifications
- Phase 18 - Assault on Lohengrin
- Phase 19 - Invisible Truth
- Phase 20 - PAST (Recap)
A recap episode explaining the event so far happened in the series and part of unexplained events in Orb from Gundam SEED, from Shinn Asuka's point of view.
- Phase 21 - Roaming Eyes
On a seemingly relaxing day, Shinn meets a girl named Stella who seems to have no past, who fell off a cliff while dancing. He jumps in the water to save her, also seeing she goes out of control from hearing the word "die". He assumes she suffered from trauma possibly from a war. They take shelter in a cave, because Stella can't swim, and they get to know each other, with Athrun rescuing them later on.
- Phase 22 - Sword From the Skies
- Phase 23 - Shadow of War
- Phase 24 - Passing Gazes
After the battle at Dardanelles that resulted the Heine's death, the Minerva returns to base for repairs. Athrun Zala temporarily leaves the Minerva to contact Archangel and her crew, through the freelance photographer Miriallia Haw. Meanwhile, Rey Za Burrel and Shinn are tasked with a recon mission on an abandoned EAF base nearby, and in disturbed by the machines and facts that they have found. Towards the end of this episode, Rey was caught in shock after seeing the cloning machinery.
- Phase 25 - Place of Sins
The abandoned facility turns out to be the factory that creates the extended pilots. The shocking truth about this creation, and the rotting stench of the bodies (revealed in the episode) is causing every ZAFT person tasked with securing the facility a trauma. On the other hand, the trio of Phantom Pain pilots got wind of the lost facility, and caused Auel to snap, and Stella to go berserk in her mobile suit, attempting to "protect the lost ones" in the facility. However, Shinn—with the help of Athrun—takes down her machine.
- Phase 26 - Promise
Stella is brought aboard the Minerva for medical treatment, while the Archangel works at getting Lacus and Andrew Waltfeld back into space.
- Phase 27 - Unreachable Feelings
Lacus and Andy reunite with the crew of the Eternal. Meanwhile the Minerva is travelling across the ocean on its way to deliver a sickly Stella to a ZAFT research facility, when they are ambushed by the joint forces of the Earth Alliance and Orb off the coast of Crete.
- Phase 28 - Remaining Life, Scattered Life
The Minerva fights the joint forces of the Alliance and Orb. The Archangel again intervenes and Kira and Athrun clash again with bad consequences for Athrun. Meanwhile Shinn decimates the Orb forces in his anger and is even able to destroy one of the stolen mobile suits. In the end he unknowingly kills a person who once helped him.
- Phase 29 - FATES (Recap)
- Phase 30 - Instant Dream
With the aid of Rey Za Burrell, Shinn takes the dying Stella from the Minerva's sickbay and returns her to Neo.
- Phase 31 - The Neverending Night
Rey and Shinn are arrested, but Chairman Durandal orders the charges dropped. Stella is given the GFAS-X1 Destroy mobile armor, and levels 3 cities, including Berlin.
- Phase 32 - Stellar
Both the Minerva and Archangel try to stop the Destroy, but Shinn hesitates when Neo tells him that Stella is the pilot. Kira manages to blow up the Destroy, fatally wounding Stella and angering Shinn. Meanwhile, Capt. Ramius encounters the defeated Neo, and receives a terrible shock.
- Phase 33 - The World Shown
Chairman Durandal makes an emergency speech, which is televised worldwide. Lord Djibril is greatly angered by the speech, which blames the Earth Alliance, Blue Cosmos and LOGOS for the attacks by the Destroy and starting another war. Meanwhile, the crew of the Archangel debates what to do with the captive Neo, who is physically identical to their fallen comrade, Mu La Flaga.
- Phase 34 - Nightmare
The ZAFT High Council pledges its' support for Chairman Durandal's new policy, while ZAFT military HQ issues orders for the Minerva to destroy the Archangel. Shinn defeats Kira and destroys the Freedom.
- Phase 35 - Chaos Ahead
Kira was able to escape the Freedom just in time, and is rescued by Cagalli. Durandal's words inspire a widespread popular uprising against LOGOS, while the damaged Archangel heads for ORB. Durandal visits the Minerva and introduces the Destiny and Legend mobile suits, which are intended as replacements for the Impulse and Saviour, respectively.
- Phase 36 - Athrun Escapes
The episode title says it all. Athrun tries to escape in a ZGMF-2000 GOUF Ignited, taking Meyrin with him, but he is pursuded by Shinn (piloting the Destiny), and Rey (piloting the Legend).
- Phase 37 - Darkness of Thunder
Shinn destroys Athrun's GOUF, but Athrun and Meyrin manage to escape. Ledonir Kisaka rescues them and brings them to the Archangel, which has returned to its' underwater port for repairs.
- Phase 38 - A New Flag
ZAFT and their allies attack Heaven's base and despite their great numbers their forces are weakened by the new LOGOS-weapon Nibelung and five Destroy units. However the situation changes when the three mobile suits of the Minerva launch and decimate the LOGOS forces. In the end Djibril flees the base.
- Phase 39 - Kira of the Sky
After the Eternal finds out about Durandal's true motives, they leave for Earth. However ZAFT discovers them and attacks. Kira helps them with the Strike Rouge and finally reunites with Lacus. He then receives the new ZGMF-X20A Strike Freedom from Lacus and disables the ZAFT units and ships chasing the Eternal with ease.
- Phase 40 - Golden Will
ZAFT attacks Orb since Djibril hides there. Orb doesn't stand a chance against the enemy forces because of the incompetence of Yuna Roma Seiran. To help the country, Erica Simmons and Ledonir Kisaka give Cagalli the new mobile suit ORB-01 Akatsuki, which was created for her by her father. Under her command the Orb forces regroup and strike back. But then she attacks Shinn.
- Phase 41 - Refrain (Recap)
- Phase 42 - Freedom and Justice
The Archangel arrives to help Orb against ZAFT. Shinn Asuka, piloting the Destiny overwhelms Cagalli Yula Athha, piloting the ORB-01 Akatsuki. Then Kira appears, piloting ZGMF-X20A Strike Freedom and helps push back the ZAFT forces.
- Phase 43 - Voice of Counterattack
Athrun launches and rushes to lend aid to Kira, who is battling Rey and Shinn. At the same time, Yuna gets crushed by a GOUF Ignited as it is defeated, when he tried to escape form his Orb escorts. Djibril manages to escape to the moon and as the ZAFT flagship is destroyed, the Minerva takes over and orders for a temperory retreat. After that battle, Cagalli broadcasts a message to Chairman Durandal. She is interrupted by Meer, who is then interrupted by the real Lacus.
- Phase 44 - The Two Lacus
The real Lacus says that there is someone who has the same face, voice and name as herself in the PLANTs. She also says that people should know more about Chairman Durandal, causing confusion over the world. After that, Chairman Durandal had was seen boarding a shuttle. Djibril is at the new Daedalus lunar base, which the Orbital All-Aspect Tactical Cannon, Requiem is located. When it is fired, it destroyed 6 PLANT colonies. It caused an uproar.
- Phase 45 - Prelude to Reform
- Phase 46 - The Song of Truth
- Phase 47 - Meer
Although Meer was killed protecting Lacus, her story lives on. Athrun, Kira, Lacus and Meyrin read the diary of Meer Campbell. Athrun laments at the loss of Meer, stating that if he had not consented to her existence none of this would have happened. Lacus swears to remember Meer and avenge her sacrifice.
- Phase 48 - To A New World
Chairman Durandal calls for the implementation of the "Destiny Plan", which is supposed to decide the fate of each individual on a genetic level. Only Orb Union and the Kingdom of Scandinavia explicitly reject this plan. ZAFT repairs Requiem and fires it at the Alliance lunar base of Arzachel, killing the president of the Atlantic Federation. Terminal forces head towards Relay Station 1 of Requiem.
- Phase 49 - Rey
Shinn and Rey are transferred to Messiah. Shinn is confronted by Durandal and Rey. Through a difficult mind struggle, Shinn finally decides to follow the course of action pointed out by Durandal and Rey. Meanwhile, Kira and Athrun destroy Relay Station 1, and Terminal forces go to attack Requiem itself.
- Phase 50 - The Final Power
Kira is confronted by Rey, who, like Rau Le Creuset, is hellbent on the destruction of Kira. However, Kira temporarily stuns him by saying that his life is his own and he does not need to be someone else. Kira then proceeds to severely cripple the Legend in one blow. Athrun, meanwhile, faces Impulse and Lunamaria, which he defeats with ease. However, Shinn comes to Luna's rescue and enters SEED mode against Athrun however he is also defeated by Athrun in SEED mode, Requiem is destroyed in a joint effort of Akatsuki and Justice.
- Final Plus - The Chosen Future (replaces Phase 50, also known as an OVA episode.)
Replaces Phase 50, also known as an OVA episode. Includes an extended battle and several new and changed scenes. Also features an alternated ending to the series which reveals what happened to the characters and the major powers after the Battle of Messiah.