The film contains newly made footage including extended sequences, the following changes have been made:
- Rau's face is shown in the laboratory sequence.
- Kira has a talk with Lacus about how he isn't sure if he wasn't meant to be born in the world after he found out the truth from Rau. Lacus responds by telling Kira he belongs to the world as long as he is born and exist in the world and his birth has made her a much happier woman, she then tells him she wants him to stay with her.
- In the final battle at GENESIS, Athrun shoots down a GuAIZ Experimental Firearms Type and a CGUE D.E.E.P. Arms from SEED-MSV.
- Clotho is killed by Dearka instead of Yzak.
- Mu La Flaga's battered helmet is removed from the debris.