Replaces Phase 50, also known as an OVA episode. Includes an extended battle and several new and changed scenes. Also features an alternated ending to the series which reveals what happened to the characters and the major powers after the Battle of Messiah.

Kira in the Strike Freedom is confronted by Rey in the Legend. Meanwhile, Athrun in the Infinite Justice battles Lunamaria in the Impulse and Shinn in the Destiny. Requiem is destroyed in a joint effort of the Infinite Justice and Mu in the Akatsuki. Due to the combined efforts of the Archangel and the Infinite Justice, the Minerva is immobilized, causing it to crash onto the Moon. Durandal and Kira confront each other in the collapsing Messiah. Durandal is shot by Rey, and Captain Gladys orders Kira to leave as she, Rey and Durandal are killed when the Messiah falls to the Moon surface. The Second Bloody Valentine War ends.

Shinn and Rey are transferred to Messiah. Shinn is confronted by Durandal and Rey. Shinn finally decides to follow the course of action pointed out by Durandal and Rey. Meanwhile, Kira and Athrun destroys Relay Station 1, and Terminal forces go to attack Requiem itself.

Chairman Durandal calls for the implementation of the “Destiny Plan”, which is supposed to decide the fate of each individual on a genetic level. Only the Orb Union, the Kingdom of Scandinavia, and the Atlantic Federation reject this plan. ZAFT repairs Requiem and fires it at the Earth Alliance lunar base of Arzachel, killing the President of the Atlantic Federation. Terminal forces head towards Relay Station 1 of Requiem.

A funeral is held for Meer on the Archangel. Athrun, Kira, Lacus, and Meyrin read Meer’s diary and learn why she had aided Durandal.