The world is divided between ZAFT and the Earth Alliance as they war against each other. But in the background, another smaller battle is about to begin.
However, as small as it may be now, if it is mishandled, it could become a gigantic wave of a war drawing the world into its wake...

MS GUNDAM SEED　VS ASTRAY　［Episode 1 Story］

Mysterious Mobile Suits appear before Junk Guild member Lowe Guele -- the Gale Strike and the Astray Red Frame. Using the group name “Librarian,” 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 mecha. 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.

MS GUNDAM SEED　VS ASTRAY　［Episode 2 Story］

A confrontation with Librarian begins at Ame-no-Mihashira as well. Mina attacks in the Astray Gold Frame Amatsu Mina. Fighting her brother Gina 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.   Meanwhile, Lowe, had been similarly attacked by Librarian, but now a new Mobile Suit appears -- the Astray Blue Frame 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!

MS GUNDAM SEED　VS ASTRAY　［Episode 3 Story］

The space station Ame-no-Mihashira. 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. 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's and once known as a ZAFT hero, Gud Vair who is now a carbon human. Elijah's mind is shaken by the appearance of his old friend. What will his conclusion be?!

MS GUNDAM SEED　VS ASTRAY　［Episode 4 Story］

Supreme Librarian Prayer gives attack orders to a certain pilot -- Lily Thevalley, a soldier specially assigned to the Supreme Librarian and given a unique mecha, the Nebula Blitz. 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 Jin 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?!

MS GUNDAM SEED　VS ASTRAY　［Episode 5 Story］

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 Red Frame Custom 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 Mirage Frame, 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.

MS GUNDAM SEED　VS ASTRAY　［Episode 6 Story］

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.

MS GUNDAM SEED　VS ASTRAY　［Episode 7 Story］

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, 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 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…?

MS GUNDAM SEED　VS ASTRAY　［Episode 8 Story］

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. They destroy colonies and engage in combat with ZAFT units. But what is their final goal...? At last, the man makes his move.

MS GUNDAM SEED　VS ASTRAY　［Episode 9 Story］

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.

MS GUNDAM SEED　VS ASTRAY　［Episode 10 Story］

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, HE realizes that Gina has discovered that Gai’s carbon human copy is HE. Battle erupts, but in that moment, a new factor appears. “Do you know Prayer Reverie?” a man comes asking. It is Canard Pars, 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.

MS GUNDAM SEED　VS ASTRAY　［Episode 11 Story］

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 arch nemesis, and HE tries to annihilate Canard, who is attempting to make a bravura 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 HE. It is a psychological trap to provoke HE and defeat Gina at the same time. Gai, Gina, HE, and Canard -- the four ace pilots now cross swords on the same field of battle.

MS GUNDAM SEED　VS ASTRAY　［Episode 12 Story］

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 Maganoikutachi − a weapon which can suck out the power of its target and absorb it for its own use. Lily immediately activates the Maganoikutachi 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.

MS GUNDAM SEED　VS ASTRAY　［Episode 13 Story］

Gai has defeated Gina. Lowe has fended off Lily. These two Astray-riders 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.

MS GUNDAM SEED　VS ASTRAY　［Episode 14 Story］(Final Episode)

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 it’s true meaning…? As the fighting is about to end once and for all, Gina appears piloting the Mirage Flame…