In the world of the Cosmic Era, war rages between the genetically enhanced humans known as Coordinators and those who remain unmodified, the Naturals, who dominate the Earth Alliance. Struggling to catch up with the Coordinators' superior technology, the Alliance secretly develops its own Gundam mobile suits. But through a twist of fate, a young Coordinator, Kira Yamato, becomes the pilot of the Alliance's prototype... and is forced to fight his own people in order to protect his friends.
- PHASE-01 False Peace
- PHASE-02 Its Name, Gundam
- PHASE-03 Collapsing Land
- PHASE-04 Phase Shift Down
- PHASE-05 The Scar of Space Part 1
- PHASE-06 The Scar of Space Part 2
- PHASE-07 The Songstress of The Enemy Forces
- PHASE-08 Stars Falling in Space
- PHASE-09 Burning Clouds of Sand
- PHASE-10 Fangs of the Enemy
- PHASE-11 Beyond the Clouds of Sand
- PHASE-12 The Sea Dyed Red
- PHASE-13 War for Two
- PHASE-14 The Land of Peace
- PHASE-15 Flash of Time
- PHASE-16 Grieving Skies
- PHASE-17 In the Promised Land
- PHASE-18 Seen and Unseen
- PHASE-19 In the Name of Justice
- PHASE-20 Decisive Fire
- PHASE-21 Into the Dawn Skies
- PHASE-22 Spiral of Encounters
- PHASE-23 The Nightmare Reborn
- PHASE-24 The Final Light
- PHASE-Final To a Future that Never Ends
- In general, the manga serves as a fast-pace version of the anime itself with scenes being combined, but it has few spelling errors such as Yzak is referred as 'Isaac' and Jachin Due is 'Yakin Doe'. Also, there is less usage of flashbacks/stock footage.
- Tolle's hair is blonde.
- Murrue did not interrogate Kira and his friends when they introduce one another, the Archangel also arrives straight away.
- Flay Allster hugs Kira in the hall corridor instead of right away in the anime.
- When Flay worries of not taking a bath, she accuses Tolle a dirtbag. Also, Kira is not around when Flay figures out that he's a coordinator.
- A comedic bath scene is added for Flay and Miriallia Haw. The boys and Mu La Flaga peeves at then, which cause them to get beat up and repriminded by Natarle Badguriel.
- The manga graphically shows a lot of dead bodies in Junius 7, as oppose to the anime which simply gives implications to some parts.
- The part of Flay interacting with Lacus is omitted, so does Kuzzey's thoughts of Flay being part of Blue Cosmos.
- Sai Argyle does not confront Flay before her attempts to held Lacus hostage.
- Kira takes Lacus back to Athrun right away under the Archangel's permission.
- Flay angrily blames Kira of her father's death on the monitor instead of face to face, but Murrue Ramius consoles Kira in not listening to her.
- Kira is around during Flay's speech of joining the Earth Alliance.
- Yzak Joule receives his scar before blasting at the refuge ship, this takes place before the Archangel lands on Earth.
- Only Flay appears in confronting Kira instead of his friends. It is unknown if Kira and Flay have sex like the anime.
- The Desert Dawn meets the Archangel right away in nightfall.
- Sai confronts Kira and Flay's relationship inside the archangel. Afterwards Flay has her thoughts of wanting Kira to die to avenge her father's death.
- Kira activates his SEED mode for the first time in Libya instead of space early on in the anime.
- Kira does not slap Cagalli at one point.
- Yzak receives the Duel Gundam Assault Shroud when going to Earth instead of earlier.
- Scenes of Phase 20 (19 in the HD Remastered) in the anime are omitted.
- Kira meets Erica Simmons after his fallout with Flay instead of the other way around.
- Athrun confronting Kira in ORB is a flashback.
- The battles of Phase 29 and 30 (27 and 28 in the HD Remastered) have been combined to one conflict. Nicol did not mention about his mother and his piano before he's killed. Athrun kills Tolle afterwards, though it does not show Tolle being decapitated like the anime.
- When Cagalli first interrogate Athrun, she initially didn't show hostility until Athrun mention the fate of the Strike Gundam's pilot.
- Sai immediately tells Flay about the situation of Kira and Tolle believing their MIA.
- As Flay attempts to shoot Dearka, Miriallia simply blocks Flays way instead of pushing her to the ground.
- Miriallia releases Dearka from his cell and tells that she's not fighting for revenge relating to Tolle, though she remains unaware that Athrun killed Tolle unlike in the anime.
- Instead of Natarle telling Flay that the war would end if everyone dies, it is Azrael in sharing his perspective of Coordinators to Flay. It shows more of Flay's initial experience and how she is horrified of the end result.
- Athrun and Cagalli never kiss before the final battle.
- Natarle is shot once by Azrael instead of many times in the anime.
- Rau speaks of giving Flay a quick death before killing her instead of being silent in the anime.
- Athrun never reunite with Patrick Zala before Athrun himself is briefly imprisoned. By the time Athrun goes inside GENESIS, he finds out his father is already dead.
- The epilogue scene in the anime is not shown.
- Vol.1 ISBN 0-34-547045-1
- Vol.2 ISBN 0-34-547179-2
- Vol.3 ISBN 0-34-547230-6
- Vol.4 ISBN 0-34-547794-4
- Vol.5 ISBN 0-34-547795-2