The report of Operation Spit Break’s failure sends the ZAFT National Defense Committee in chaos. At the same time, Patrick Zala learns that the latest MS Freedom Gundam, which was secretly developed by ZAFT, was stolen. He tells his son Athrun, who was called back to the homeland, that Lacus helped steal it; that she is wanted for treason, and she is no longer his fiancé. Athrun is taken aback. Chairman Zala fails to keep the annoyance out of his face and orders Athrun to eliminate Lacus and anyone connected to the theft of the Freedom Gundam.
Meanwhile, in Alaska, where the Cyclops system was detonated, the Archangel was saved by Kira and he was reunited with the joyful crew. But Kira’s heart was searching for the purpose to fight in this war ever since his reunion with Lacus.
As if guided by Haro, Athrun is reunited with Lacus at an abandoned concert hall and learns that Kira is alive. He is beyond shocked. Lacus asks a cryptic question saying, “What are you fighting for?” and leaves.
Athrun takes Justice Gundam and head to Earth, to face Kira once again…