The discovery of an advanced model of combat mecha on their space colony throws a young man and his friends into involvement in an interplanetary war as the crew of a powerful fighting ship.
Lacus Clyne, the daughter of PLANT Supreme Council Chairman Siegel Clyne, is found within the lifepod. Her presence causes tension within the crew, but when the crew receives a message from the 8th Fleet that they are being searched and rescued, they are overjoyed.
A recap of the first 25 episodes. Narrated by Tony Sampson, Miguel Aiman's voice actor (in the Japanese version it is narrated by Takanori Nishikawa, Miguel's Japanese voice actor) (NOTE: omitted in the HD Remastered version, making Endless Rondo episode 25).
Rau Le Creuset reflects on the events that took place in episodes one to thirteen and the Coordinator's history starting from the birth of the First Coordinator, George Glenn (NOTE: This episode is omitted in the HD Remastered version, making The Respective Solitudes episode 14).
The crew of the Archangel find themselves questioned for their actions regarding their escape from Heliopolis, the fall of the 8th Fleet, and entrusting the Strike to Kira Yamato. Meanwhile, Lacus comforts Kira, who questions his right to live, especially after trying to kill Athrun.
Mu La Flaga and Kira launch a counteroffensive against the ZAFT ship Vesalius. The Strike's Phase Shift Armor runs out of power in the middle of the battle and Athrun uses this moment to grab the Strike so he can take Kira with him, but Kira frees himself with Mu's help.
Senior Engineer Erica Simmons of Morgenroete reviews the Strike's combat logs and theorizes that Kira might be superior than any other Coordinator and speculates on the "SEED factor" theory. She shows Kira the mobile suits that Orb is developing and asks him to develop a mobile suit operating system that can be used by Naturals.
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.
Lt. Murrue Ramius takes over as captain of the Archangel and Kira and his friends are detained for seeing top secret military weapons. Rau Le Creuset is determined to capture the Strike after seeing how well it moved and sends out mobile suits to retrieve it. Disobeying orders, Athrun also dispatches so he could confirm if Kira is the one piloting the Strike, but when he finds his answer, Heliopolis crumbles as it sustains too much damage.
Cagalli, though grief striken with her father's death, confronts Kira with a mysterious photograph given to her by Lord Uzumi, of a woman with two infants and Kira and Cagalli's names written on the back. On a PLANT, Lacus is still on the run for treason, but broadcasts messages to counter PLANT Supreme Council Chairman Patrick Zala's propaganda. She soon discovers that her father has been assassinated by Patrick Zala.
The Archangel and its crew are held captive by the Artemis forces. Nicol Amalfi in his GAT-X207 Blitz attacks Artemis, using its Mirage Colloid armor to remain effectively invisible and destroys the Umbrella of Artemis, which protects the asteroid fortress. During the attack, the Archangel is able to escape.
The crew of the Archangel grieve for the apparent deaths of Kira and Tolle. Cagalli searches the wreckage for Kira but instead finds Athrun and confronts him for killing Kira.
The Archangel is attacked by multiple TMF/A-802 BuCUE units. Kira hastily takes off and fights the ZAFT forces, but he is unfamiliar with the desert environment. His ability to adapt amazes ZAFT's commander Andrew Waltfeld. When the Strike is about to run out of power, a resistance group comes to his aid and lures the remaining BuCUE units into an explosive trap.
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.
The Archangel is attacked by the Zala Team which consists of the Le Creuset Team members. They take heavy damage, but when they enter the waters of the neutral nation of Orb, ZAFT is chased away and is told that the Archangel has been chased away. The Zala Team sneaks into Orb with the belief that Orb's official statement is false.
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.
The newly-formed Three Ships Alliance take shelter at the abandoned Mendel colony. Unfortunately, they are tracked down by both ZAFT and Earth Alliance forces. Rau Le Creuset commands the ZAFT fleet and Captain Natarle Badgiruel, commands the Earth Alliance assault ship Dominion. Dominion takes the initiative and attacks with the mission of capturing either the Freedom or Justice.
Athrun in the Justice assists Kira fight against the Forbidden, Raider, and Calamity. As the fight continues, the three Earth Alliance pilots argue with one another, but they are interrupted when they are struck by intense pain. The Earth Alliance are forced to retreat and regroup. The two friends reunite and Athrun must make a decision regarding whether he should continue obeying his father's orders or fight for what he believes in.
Kira and his friends are given permission to leave the Archangel, but after overcoming the initial shock of her father's death, Flay decides to enlist in the Earth Alliance Forces, prompting Sai Argyle, Kuzzey Buskirk, Miriallia Haw, and Tolle Koenig to do the same. Kira stays on board the as well to continue protecting his friends. Duel Gundam is upgraded with an Assault Shroud.
The Archangel is to meet with the 8th fleet but is attacked by the Le Creuset Team. Flay witnesses the death of her father when Kira fails to protect the escort ships. In desperation, the Archangel reveals Lacus is on board the ship, causing the attackers to withdraw.
Murrue Ramius thanks the resistance group for their help and agrees to be allies. The resistance group introduces themselves as the Desert Dawn who are fighting Andrew and the Lesseps. Kira once again meets with Cagalli Yula Athha, the mysterious young woman he first encountered at Heliopolis' Morgenroete factory, who is now part of Desert Dawn. Meanwhile, Andrew attacks the Desert Dawn's hometown, but evacuates the town first.
ZAFT is able to steal four of the five G Project prototype mobile suits, leaving only the GAT-X105 Strike. With Murrue Ramius unable to pilot it effectively, Kira pilots the Strike and defends Heliopolis against the invading ZAFT forces to protect his friends. Ensign Natarle Badgiruel takes command of the new mobile assault ship Archangel with the surviving crew members.
Kira and his friends are given the chance to meet with their parents who have taken refuge in Orb. Kira refuses to go, but his parents meet with Uzumi Nara Athha who hints there is a deeper connection between Kira and Cagalli. Kira instead completes the operating system for the Orb Union's MBF-M1 Astrays. When Kira's mechanical bird flies off, Kira finds himself standing face to face with Athrun. They part ways pretending not to know each other, but not without saying kind words about each other.
Flay, Mu, and Natarle are to be transferred off the Archangel. Mu suspects that something is not quite right as the Alaskan JOSH-A base is evacuated. Flay is captured by Rau Le Creuset. Lacus and her father entrust Kira with the ZGMF-X10A Freedom, equipped with Neutron Jammer Canceller technology.
Kira and the Archangel make their way to Orb, where Lord Uzumi welcomes them and asks that they decide for themselves why they are fighting. The Panama mass driver is destroyed by ZAFT in retaliation for the blow they took at Alaska. Meanwhile, Erica Simmons presents a reconstructed Strike for the Archangel crew's use.
Athrun returns to the PLANTs on a shuttle to speak to his father, but he is arrested. Lacus and (the presumed killed in action) Andrew Waltfeld join forces, stealing the ZAFT support ship Eternal and rescuing Athrun. They join forces with the Archangel and the Kusanagi thus forming the Three Ships Alliance.