The Archangel forages for water in the Debris Belt. They are shocked to find themselves in the ruins of Junius Seven, so the crew decides to hold a memorial. As they are excavating ice found around the ruin, a ZAFT mobile suit attacks, but Kira dispatches him. Kira finds a floating lifepod and takes it aboard.

Athrun and Nicol are given the day off; Athrun spends the day with Lacus and they talk about Kira. The PLANT Supreme Council debates on whether the attack codenamed "Operation Spitbreak" should be executed

The Archangel crew crosses the Red Sea to head towards the neutral Orb Union with Cagalli and Ledonir Kisaka on board. With the previous battle weighing heavily on him, Kira talks to Cagalli about his reasons for fighting, making Flay jealous. They are attacked by ZAFT air and underwater type mobile suits, but Kira and Mu manage to take them out.

The Archangel finally arrives in Alaska. A grief-stricken Miriallia attacks Dearka, now a prisoner on board the Archangel, but ends up saving his life when Flay tries to shoot him. Kira awakes and finds himself in the care of Lacus.

Lacus, now denounced a traitor to the PLANTs for handing the Freedom over to an unknown pilot, confronts Athrun and challenges him to decide what he truly is fighting for. Athrun is ordered to pilot the ZGMF-X09A Justice to seek and destroy the Freedom.

The Earth Alliance attacks again, but the results are the same as the previous battle. The Archangel and the Orb ship Kusanagi launch into space, while the leaders of Orb stay behind. They explode Orb's mass driver and armaments factories, sacrificing their own lives in the process.

Equipped with Neutron Jammer Cancellers, the Earth Alliance forces launch an all-out attack on the PLANTs. The Boaz military asteroid is destroyed by nuclear weapons with Earth Alliance's next target being the PLANTs. The Freedom and Justice arrive at the battlefield in time to destroy all the nuclear warheads. In retaliation, Patrick Zala orders to fire the GENESIS.

An animated short featuring the characters and mecha of the Astray R manga/novel series, as well as mobile suits from the Gundam SEED MSV (Mobile Suit Variations) model kit series.

A short special, set between the end of Gundam SEED and the beginning of Gundam SEED Destiny, showing what happened to the characters.

An animated short featuring the characters and mecha of the Astray B manga/novel series, as well as mobile suits from the Gundam SEED MSV (Mobile Suit Variations) model kit series.

A special recap, that analyzes the events of the series following operation "Break the World" and military strengths of ZAFT, Orb & the Atlantic Federation. This episode does not appear on the DVD release.

The Archangel and its allies are now humanity's last hope to prevent Durandal from carrying out his Destiny Plan. Once again, a fierce battle begins around the Requiem cannon and its relay stations, and the Gundam pilots meet in a final confrontation over the lunar surface. Shinn against Athrun, Kira against Rey, Archangel against Minerva... In the end, there can be only one victor.

Extended cut of SEED Destiny's series finale released as an OVA.