Cosmic Era 73. Though the signing of a peace treaty brought the war between the Naturals and Coordinators to an apparent close, tensions fueled by the continued threat of Blue Cosmos continue to run high. During a conference between PLANT chairman Gilbert Durandal and Orb representative Cagalli Yula Athha concerning the threat of a new military arms race, an Alliance special forces team attacks the ZAFT base they're meeting at and makes off with three new Gundam mobile suits. Forced to pursue them, Shinn Asuka of ZAFT and Athrun Zala of Orb set out aboard the new space battleship Minerva, and engage the retreating Alliance strike team in combat. But just as they catch up to the fleeing ship, the crew of the Minerva receives word of an even greater catastrophe in the making, which will undoubtedly re-ignite the brutal war between the Naturals & Coordinators all over again.
- PHASE-01 Angry Eyes
- PHASE-02 The end of the World
- PHASE-03 Junction
- PHASE-04 The Sea turns Red with Blood
- PHASE-05 Return to War
- PHASE-06 Mortal Combat over the Indian Ocean
- PHASE-07 The Hidden Truth
- PHASE-08 The Shadows of War
- PHASE-09 The House of Sin
- PHASE-10 Stella
- PHASE-11 Seen by the World
- PHASE-12 Athrun's Escape
- PHASE-13 The Golden Will
- PHASE-14 Freedom and Justice
- PHASE-15 Prelude for Change
- PHASE-16 A new World
- PHASE-17 Rey
- PHASE-18 Tomorrow never Ends
- In general, just like its predecessor, the manga serves as a fast-pace version of the anime itself with scenes being combined. There are less flashbacks shown unlike in the anime.
- Stella, Sting, and Auel did not kill people before they steal the Gundams.
- Shinn takes out his anger and insults to Cagalli only once.
- The flashback showing the deaths of Shinn’s family happens later instead of first seen in the prologue.
- Kira doesn’t joke Cagalli of her wedding dress.
- Athrun slaps Shinn privately outside of the ship instead of public, and their time and conversation combines Episode 16 and 17 to one scene.
- Shinn and Stella did not rest in the night and remain clothed when Stella is sent back to her two comrades straight away.
- Luna does not spy on Kira and Athrun’s debatable conversation.
- When Athrun punched Shinn, they did not about to start a fight unlike the anime.
- Shinn and Luna did not kiss.
- After getting shot, Meer did not ‘act like dancing around’ before falling down.
- There is a brief conversation of Athrun consoling Shinn as the final scene with Luna joining the two too leave the moon.
- There is no epilogue scene such as Shinn and Kira personally meet.
When the manga was released in English by Del Ray, it caused an uproar due to the fact that it blatantly spelled characters, units and places in stark contrast to the original Gundam SEED manga and the official names. The official plot summary is also wildly inaccurate, referring to PLANT as the "ZAFT Empire", and saying that Neo Roanoke and the ZAFT terrorists plotted the Junius Seven drop together. From the second volume onward, there was an author's note explaining the reasoning for the changed spellings.