The world is divided between ZAFT and the Earth Alliance as they war against each other. In the background, another smaller battle is about to begin and if it is mishandled, it could become a gigantic wave of a war drawing the world into its wake...
An organization going by the name "Librarian Works" appears before the Junk Guild, Serpent Tail and to Rondo Mina Sahaku. The group demanded the three factions to surrender not just their mobile weapons, but also everything they have. A revived Rondo Gina Sahaku is seen as part of the organization and is waiting to get his revenge against Gai Murakumo. Carbon Humans piloting modified ZAFT and EA Mobile Suits were dispatched to fight against the three factions.
Episode 1 Story: Phantom
Mysterious Mobile Suits appear before Junk Guild member Lowe Guele—the LG-GAT-X105 Gale Strike Gundam and the MBF-P02 Gundam Astray Red Frame. Using the group name “Librarian,” a mysterious Military Organization ruled by a mysterious person, they demand Lowe surrender to them completely. When Lowe refuses, his battle with Librarian begins. The enemy Red Frame turns out to have been built using data copied from his own machine, and its pilot is none other than Un'no, the man who once taught Lowe swordsmanship! Why was this man who was supposed to be dead here now...?
Meanwhile Librarian appears before Rondo Mina Sahaku at Ame-no-Mihashira as well. Lowe battles his master Un'no and defeats him and damages the replica Red Frame. The Gale Strike's pilot, the masked Librarian pilot ND-HE, rescues Un'no and retreats.
Episode 2 Story: Slash with a Sharp Sword
A confrontation with Librarian begins at Ame-no-Mihashira as well. Rondo Mina Sahaku launches in the MBF-P01-Re2AMATU Gundam Astray Gold Frame Amatsu Mina. Fighting her brother Rondo Gina Sahaku had been an agonizing decision for her, but she was unable to come to terms with his obsessively old ways of thinking. Gold versus Gold, the flames of battle are lit by brother and sister. Gina in his MBF-P01 Gundam Astray Gold Frame built using data copied from the original battles Mina in her Astray Gold Frame Amatsu Mina. Meanwhile, Lowe, had been similarly attacked by Librarian, but now a new Mobile Suit appears -- MBF-P03R Gundam Astray Blue Frame 2nd Revise. It is the new weapon of Gai Murakumo, leader of the mercenary military group Serpent Tail. Gale versus Revise—the two giant weapons now clash in battle! The Lowe piloting the Astray Red Frame battle Gai in his Astray Blue Frame Revise. After the battle Gai heads towards the space station Ame-no-Mihashira to seek some answers of why there two Astray Red Frame.
Episode 3 Story: Old Friend
The space station Ame-no-Mihashira. Mina and Gina are battling each other. Mina is unable to kill her brother, but Gai appears in the Astray Blue Frame Revise. There Rondo Gina Sahaku faces off against Gai Murakumo. An almost abnormal hate burns in Gina towards Gai—the man who once sent him to his grave - and the two begin battling. Meanwhile, a Librarian assassin appears before members of the mercenary group Serpent Tail who had remained on the surface as well. "Elijah, come to Librarian!" says a man who was once a dear friend of Elijah Kiel's and once known as a ZAFT hero, Gud Vair who is now a carbon human. Elijah's mind is so shaken by the appearance of his old friend that he has second thoughts on killing him, even thought he was a Carbon Human Clone. Elijah piloting his ZGMF-1001 Elijah's ZAKU Phantom battles Gud Vair in his LV-ZGMF-X23S Vent Saviour Gundam. At the space station Ame-no-Mihashira, Gina battles Gai, but ends up losing once again.
Episode 4 Story: Lily Thevalley
Gina has upgraded his Astray Gold Frame into MBF-05LM Gundam Astray Mirage Frame and goes off to battle Gai in his Blue Frame Second Revise. Supreme Librarian Prayer Reverie gives attack orders to a certain pilot -- Lily Thevalley, a soldier specially assigned to the Supreme Librarian and given a unique mecha, the LN-GAT-X207 Nebula Blitz Gundam. Against the attack, Un’no attempts to fight her to test Lily’s strength. However, in the blink of an eye, Lily in the Nebula Blitz crushes Un’no who had attacked with a Japanese Katana-equipped Ginn High Maneuver Type 2. Meanwhile, the battle between Gina and Gai is nearing its decisive moment. Which Astray—the Mirage Frame or the Blue Frame Second Revise—will seize victory?!
Episode 5 Story: Frenzy
Elijah vs. Vair. The battle between these two once dear comrades approaches a conclusion no one could have imagined. Meanwhile, anticipating another Librarian attack, Lowe upgrades his mecha and the MBF-P02Kai Gundam Astray Red Frame Kai is completed. Assisting him were many members from the past. And there is another Astray mecha which has been powered-up as well: Rondo Gina Sahaku’s MBF-P05LM2 Gundam Astray Mirage Frame 2nd Issue, which lost in battle to Gai’s Blue Revise. To pilot this strengthened beyond belief “Second Issue,” Gina has an upgrade to his own physical body as well.
Episode 6 Story: Teleport
Having been beaten in combat by Gai, Rondo Gina upgrades his Mirage Frame turning it into a “Second Issue”—a mecha of uncontrollable speeds. In order to be able to pilot it, Gina upgrades his own physical body as well. After completion, Gina boards the Second Issue, but his attack is halted by the Nebula Blitz under the direct control of Prayer the Supreme Librarian. The two enter into battle, but at the same time an enemy appears where Lowe has just completed the Red Frame Kai as well. Incredibly, it is the Nebula Blitz, piloted by Lily, which is supposed to be off fighting with Gina at that same moment.
Episode 7 Story: Astray vs. Astray
In the Red Frame Kai, Lowe battles Lily’s Nebula Blitz. While at the mercy of its teleportation capability, he realizes the secret behind it and is able to beat her. Meanwhile, ND-HE approaches Prayer, the Supreme Librarian. “Why are there so many betrayals like this?” he asks. It is an unnatural thing for an organization. To get his answer, Prayer sends ND-HE to travel with Rondo Gina. Gina was then on the verge of destroying the Nebula Blitz which was trying to restrain the ignoring of orders. But what was behind the actions of the traitorous Gina…?
Episode 8 Story: Remodeled Machine
Having ascended to space, Elijah meets junk dealer Lowe Guele along with Gai. They mutually exchange information on Librarian and also customize the Vent Savior they have acquired for Elijah’s own use. Meanwhile, Lowe has rescued Lily Thevalley, the pilot of the Nebula Blitz which Lowe defeated. He is a junk dealer. He doesn’t want to take a life, even that of an enemy he has beaten in battle. At the same time, Librarian activity intensifies the world over. Kaite Madigan a mercenary piloting LR-GAT-X102 Regen Duel Gundam, Finis Socius a coordinator produced by the Alliance pilots LH-GAT-X103 Hail Buster Gundam, and Supreme Librarian Prayer Reverie piloting LN-ZGMF-X13A Nix Providence Gundam. They attack, destroy colonies, and engage in combat with ZAFT units. But what is their final goal...? At last, the man makes his move.
Episode 9 Story: The Real Face Underneath the Mask
In order to settle things with Gai Murakumo once and for all, Rondo Gina Sahaku steps away from Librarian and begins making moves on his own. HE, traveling along with him, has a grave secret. Gina, traveling with HE, discovers who he is a Carbon Human copy of. Unable to allow his continued existence, Gina launches an attack against him. Gina’s Second Issue and HE’s Gail Strike—two Librarian mecha specialized for close combat—begin a mortal struggle. Meanwhile, having failed in her attack against the Junk Guild, Lily is saved by Lowe. Placed among the members of the Junk Guild, Lily is disoriented by their unpretentious personalities, but at the same time feels their warmth. However, a new Librarian attack squad appears. Steeling her resolve, takes off into battle in still-being-repaired Gold Frame Amatsu.
Episode 10 Story: Gai vs. Gai
Reed and Loretta of Serpent Tail try to make sense of information they’ve gleaned on the mysterious enemy Librarian. Among it emerges the truth about the carbon human, but what is it? Meanwhile, ND-HE realizes that Gina has discovered the truth of his identity. The battle between Gina and ND-HE enters an unforeseeable stage, as ND HE is revealed as a carbon human clone of none other than Gai Murakumo. The battle between Gina and ND-HE is interrupted by a man asking “Do you know Prayer Reverie?”. It is Canard Pars piloting YMF-X000A/H Dreadnought H, is a man who had fought for his very life alongside Prayer. Canard possesses abilities on par with a super coordinator, and with his entry into the war, the flow of battle will change dramatically. He ask both Gina and ND-HE if they know where to find Prayer Reverie. Elsewhere, Lily is attacking in the Gold Frame Amatsu and must fight against Lily herself. The destiny of each battle is thrown into great disorder.
Episode 11 Story: X Astray
Librarian members Gina and HE are working together. Before them appears Canard Pars seeking to end the life of Supreme Librarian Prayer. In a war zone searing with the tensions of battle, Gai Murakumo suddenly bursts onto the scene with the Blue Frame Revise. Gina is driven into a frenzy by the entrance of his nemesis, and HE tries to annihilate Canard, who is attempting to make a brave show of strength in front of one who should be his superior. The thoughts of all the participants sweep through the battleground. In the middle of the maelstrom, Gai’s line of sight turns to ND-HE. It is a psychological trap to provoke ND-HE and defeat Gina at the same time. Gai, Gina, ND-HE, and Canard—the four ace pilots now cross swords on the same field of battle.
Episode 12 Story: Original and Copy
The space station of the Junk Guild’s Lowe Guele. The Librarian assassins who appear there are in four Nebula Blitzes. Lily, who had been saved by Lowe, sets out in the Gold Frame Amatsu to try to halt the battle. However, the enemies turn a deaf ear to Lily’s desperate arguments. The four mecha actuate their Maga-no-Ikutachi － a weapon which can suck out the power of its target and absorb it for its own use. Lily immediately activates the Maga-no-Ikutachi equipped on the Gold Amatsu as well and counterattacks. But overwhelmed by their numbers, she is gradually losing power when reinforcements appear － Elijah piloting the Vent Saviour.
Episode 13 Story: New War
Gai has defeated Gina. Lowe has fended off Lily. These two Astray pilots are joined by Canard, and with HE’s guidance, the three of them head for the Librarian home base. And the one they are aiming for is the organization’s Supreme Librarian, Prayer Reverie. Eventually, they come upon the headquarters, camouflaged in an asteroid. Unexpectedly, Prayer allows the three to pass inside. What will Canard do now face-to-face with the instigator of all the events that have come to pass? And, who will Lowe come into contact with, now that he is operating separately from the others inside the base…? The war now enters its final phase.
Episode 14 Story: Last War
In order to settle things once and for all through combat, Supreme Librarian Prayer launches into space in a mobile suit. Gai and Lowe engage him, along with Canard. Prayer’s Nix Providence equipped with the DRAGOON displays overwhelming power, but before Canard and Gai working in tandem his defeat becomes decisive. But in that moment, Prayer confesses Librarian’s true goal and what Prayer has been trying to achieve is revealed. With Prayer’s defeat, he is trying to accomplish that goal. What could be its true meaning…? As the fighting is about to end once and for all, Gina appears piloting the Mirage Frame, which has been upgraded once more…
- Lowe Guele - A Natural, he is an excellent engineer, technician, and pilot of the MBF-P02 Gundam Astray Red Frame. First operated from the HOME, with the Professor, Kisato Yamabuki, and Liam Garfield; later transferred to ReHOME.
- Kisato Yamabuki - Natural, fellow Junk Tech with Lowe, Liam, and the Professor. She has the hobby of collecting memorabilia of the First Coordinator George Glenn. She lacks self-confidence and easily frightened when there is fighting, pilots a custom Kimera and later a modified version of the BuCUE Andrew Waltfeld Custom.
- 8 - Artificially Intelligent computer found by Lowe on a drifting spacecraft, it is named for the only visible writing on its casing. Serves as a co-pilot for Lowe Guele's Gundam Astray Red Frame and later Jess Rabble's Gundam Astray Out Frame. Jess later returns 8 to Lowe.
- Liam Garfield - As the Garfields wanted to bridge the gap between Naturals and Coordinators, Liam was born as a Coordinator while his twin brother is a Natural. Due to his unique background, he has a habit of observing the Naturals' behaviors (especially Lowe). He pilots a customized Kimera and a Works GINN. He is later elected as Chairperson of the Junk Guild.
- The Professor - atural; real name and her past unknown. A brilliant scientist and captain of the Marseille III-class ship, HOME, she is also a close friend of Morgenroete's Erica Simmons. She later creates a holographic body for George Glenn so that she won't have to bother with commanding the new Cornelius-class ship, ReHOME.
- Yoon Sefan - Natural; clumsy former Morgenroete Inc. engineer, joined the Junk Guild after being left behind during the evacuation of Orb before its destruction at the hands of EA forces. Designer of the MWF-JG71 Raysta, a civilian-use mobile suit, and pilot of a custom Raysta.
- Gai Murakumo - Coordinator, a shrewd mercenary with excellent battle sense and the leader of the Serpent Tail mercenary company, and pilot of the MBF-P03 Gundam Astray Blue Frame, MBF-P03secondL Gundam Astray Blue Frame Second L and their variants. He first meets Lowe Guele at the remains of Heliopolis. Nobody knows his past, where he was actually a Combat Coordinator developed by the Earth Alliance. His combat abilities were completed at a high level, but his mental control was incomplete when he escaped the research facility. A "1" can be found on the Serpent Tail emblem on his mobile suit.
- Elijah Kiel -Coordinator and Gai's wingman, pilots the ZGMF-1017 Elijah's GINN and later the ZGMF-1001 Elijah's ZAKU Phantom. Previously, he was with ZAFT. He has a very handsome look, but although he is a Coordinator, he does not possess the superior physiology of Coordinator. As such, his MS maneuvering skills are poor initially, but through the experiences he gained on the battlefield as a mercenary, his skills have improved substantially. A "2" can be found on the Serpent Tail emblem on his mobile suit.
- Kazahana Adja - 6 years old and highly intelligent daughter of Loretta. Due to her background, she has adult-like judgement and mental toughness. She serves as liaison to Serpent Tail's clients. Unknown if she is a Natural or Coordinator.
- Loretta Adja - Natural, mother of Kazahana Adja and the only woman among members of Serpent Tail. She is an explosives expert and tactician. She is very popular among the mercenaries, and previously works for EA, unknown why she left.
- Reed Wheeler - Natural; captain of Serpent Tail's Laurasia-class frigate. He was a former Earth Alliance intelligence operative and still has contacts within the EA. A known alcoholic.
- Rondo Mina Sahaku - Coordinator; co-head of the Sahaku family of the Orb Union and twin sister of Rondo Gina Sahaku. More empathetic and calm than her brother. She pilots the MBF-P01-Re2AMATU Gundam Astray Gold Frame Amatsu Mina.
- ND HE(NO DATA HIGH ERROR) - ND HE (also known as NO DATA-HIGH ERROR) is a Librarian pilot in Mobile Suit Gundam SEED vs Astray. A carbon human created to facilitate the organization's activities. He wears a helmet-like mask in his head. Because his face is always hidden behind a mask, his true identity is not knowable from his outward appearance, but his combat ability and piloting senses are exceptional. He's a Carbon Human Clone of a young Gai Murakumo. Pilots LG-GAT-X105 Gale Strike Gundam.
- Finis Socius - Finis Socius is a Librarian pilot in Mobile Suit Gundam SEED vs Astray. A coordinator produced by the Alliance, but this is a newly created Socius. Pilots LH-GAT-X103 Hail Buster Gundam.
- Kaite Madigan - Coordinator and professional MS pilot. Pilots multiple customized mobile suits manufactured by the EA and ZAFT depending on the missions. Very confident in his abilities, and he always wears a business suit even in battle. Pilots LR-GAT-X102 Regen Duel Gundam.
- Prayer Reverie - A person of high status within Librarian. He appears to be the same Prayer Reverie who once acted alongside Lowe Guele and his team, but the truth of whether it is actually him or a carbon human is kept secret even within the Librarian organization. Pilots LN-ZGMF-X13A Nix Providence Gundam.
- Rondo Gina Sahaku - A carbon human version of Rondo Gina Sahaku the co-head of the Sahaku family of the Orb Union. Highly aggressive pilot of the MBF-05LM Gundam Astray Mirage Frame and later the MBF-P05LM2 Gundam Astray Mirage Frame 2nd Issue.
- Lily Thevalley - Lily Thevalley is a carbon human not copied from a specific person, but she is skilled enough to make her more than an even match in combat against famous pilots. She is in the special brigade assigned to Supreme Librarian Prayer Reverie. She pilots the LN-GAT-X207 Nebula Blitz Gundam.
- Canard Pars - Coordinator; ex-Eurasian Federation ace pilot and "Special Forces" member, now mercenary and pilot of YMF-X000A/H Dreadnought H. Initially served as a mercenary with the Serpent Tail, but left to lead his own mercenary group.
- LG-GAT-X105 Gale Strike Gundam
- LH-GAT-X103 Hail Buster Gundam
- LN-ZGMF-X13A Nix Providence Gundam
- LR-GAT-X102 Regen Duel Gundam
- LV-ZGMF-X23S Vent Saviour Gundam
- LN-GAT-X207 Nebula Blitz Gundam
- MBF-05LM Gundam Astray Mirage Frame
- ZGMF-1017M2 GINN High Maneuver Type II
- MBF-P02 Gundam Astray Red Frame
- LN-GAT-X207 Nebula Blitz Gundam
- MBF-P03R Gundam Astray Blue Frame 2nd Revise
- ZGMF-1001 Elijah's ZAKU Phantom
- LV-ZGMF-X23S Vent Saviour Gundam
- Seed vs Astray official website (English)
- Seed vs Astray official website (Japanese)