The film contains newly made footage including extended sequences, the following changes have been made:
- A brand new 55 second scene showing preparation for the assault on Heliopolis (shows more shots of Miguel and new shots of Rusty).
- Scenes of Kira and his friends before the going off were redone.
- Newtype flash added when Mu senses Creuset for the first time
- Footage of GINN's battling with Moebius mobile armors outside the colony, has been removed.
- Debut of Cagalli is retold and a new scene of her conversation with Kira with new footage
- Athrun and Kira's first meeting during the firefight in episode 1 intercuts with scenes when they were kids instead of being shown slowly with negative colors.
- Scene of Flay emerging from the lifepod (ep 4) and hugging Kira is redone and retold. Also a new 30 second scene of Sai and Flay conversing has been added.
- The scene with Rau and Athrun discussing the Strike's pilot is reduced to a 10-second flashback and is inserted into the scene where Athrun is lying and thinking about the loss of Rusty and Miguel.
- The Archangel's heading to Artemis and the Battle of Artemis footage had been removed.
- Athrun's shower scene (ep 8) is lengthened and intercut with scenes of his parents; and the scene following this (his discovery of Lacus' disappearance) is completely redone and moved to be ahead of hatch opening sequence of Lacus's life pod.
- Backstory from the first clip show is never told.
- New 25 second clip of Lacus trip to the cafeteria on board the Archangel.
- The scene of Rau and Mu taking the opportunity to attack during the time that Kira is transferring Lacus to Athrun only for Lacus to order Rau to stand down and withdraw is removed.
- Scene of Kira having sex with Flay is shown cut between Strike's first battle in the desert with additional new footage.
Cagalli's bath sequence is changed from a bath to a shower instead, probably for fanservice.
- The scenes of Dearka and Yzak assisting Andrew Waltfeld during his final attack on the Archangel have been removed.
