| ShortSummary | - After the Eternal learns Durandal's true motives, the ship is discovered by ZAFT forces and a battle ensues. Kira helps them with the Strike Rouge and reunites with Lacus. He then receives the new ZGMF-X20A Strike Freedom from Lacus and disables the ZAFT units and ships chasing the Eternal with ease.
- Lt. Murrue Ramius takes over as captain of the Archangel and Kira and his friends are detained for seeing top secret military weapons while the crew of the Archangel learn that Kira is a coordinator. 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 stricken 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.
- Kira discovers a malfunctioning lifeboat and brings it aboard the Archangel. Everyone is surprised to find Flay Allster as one of the rescued civilians. The Archangel decides to head for the Eurasian Federation military satellite Artemis to seek help. Rau Le Creuset follows and plans an attack on the Archangel. Kira decides to continue piloting the Strike and his friends volunteer to become members of the Archangel crew as his support.
- The Archangels escort to meet with the 8th fleet 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.
- Athrun is reinstated in the ZAFT military and appointed to FAITH. He is given the Saviour mobile suit and assigned to the Minerva. Captain Gladys is also appointed to FAITH, which creates something of a conflict in the command structure; Athrun and she now have more or less equal rank and strategic authority.
- The Minerva comes under attack again. But this time the Earth Alliance Forces are being assisted by the Orb forces. Seeing that they are cornered Captain Gladys orders the Minerva to fire the Tannhäuser. The Archangel arrives.
- 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.
- Shinn meets a girl named Stella Loussier, who fell off a cliff while dancing and seems to have no past. He jumps into the water to save her, also seeing she goes out of control from hearing the word "die". He assumes she suffers from trauma possibly from a war. They shelter in a cave, because Stella can not swim, and get to know each other, with Athrun rescuing them later on.
- Athrun talks with Gilbert Durandal about the attack on the PLANTs and what his plans are. Because the people in the PLANTs are outraged, a Lacus look-alike hired by Gilbert Durandal calms the people. Athrun decides to do something and Durandal shows him the new ZGMF-X23S Saviour and offers him the chance to become its pilot. Afterwards Athrun meets the fake Lacus again, Meer Campbell.
- 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.
- 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.
- Covers the events of Gundam SEED Destiny Phases 14 to 28.
- While the Minerva crew praises Shinn for his incredible fight, Orb joins the Earth Alliance much to Cagalli's abhorrence. Meanwhile, Kira and his friends are attacked by Coordinators who attempt to assassinate Lacus using the new UMF/SSO-3 ASH mobile suits. Kira reactivates the Freedom to protect his friends. Although he only disables the enemy mobile suits, the assassins activate self-destruct mechanisms for their mobile suits.
- The Minerva enters Orb where the ship is to be repaired. While this takes place Talia Gladys meets with Maria Bernes; also known as Murrue Ramius. Meanwhile, the Orb government is considering an alliance with the Earth Alliance much to Cagalli's dismay. Athrun meets Kira and Lacus. Athrun and Kira discuss what he witnessed in the ruins of Junius Seven and how he plans to go to the PLANTs. Shinn visits a memorial at Orb and meets Kira and Lacus.
- As the attack on Orb continues, Cagalli faces off against Shinn. She is saved by the timely arrival of Kira who descended from space with Lacus. Shinn is forced to retreat to resupply. While Kira continues to destroy ZAFT forces, Lacus shows Athrun the ZGMF-X19A Infinite Justice and gives him the decision to choose whether he wishes to stay away from the battle or become a soldier again and fight for what he believes in.
- Flay, who was held captive by Rau, is rescued by the Dominion despite Kira's desperate attempts to steal her lifepod. She gives Muruta Azrael the disk she was given by Rau which contains the specs on the Freedom and Justice and the Neutron Jammer Canceller technology.
- 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.
- Operation Spitbreak is initiated, with both ZAFT and the Earth Alliance believing they have outsmarted the other. The Archangel is left behind to be destroyed in a calculated plan that would decimate everyone on the battlefield, until Kira arrives to save them.
- The new ZAFT battleship Minerva chases the Girty Lue. Meanwhile, Cagalli and Athrun are led through the ship by Durandal but Cagalli is confronted by an angry Shinn. They find the enemy ship and the Minervas mobile suits are ordered to launch.
- Stella's condition worsens and Shinn overhears Captain Talia telling a doctor that the PLANT Supreme Council wants a living extended and Stella won't be living much longer. With the help of Rey, Shinn forcedly takes the dying Stella from the Minervas sickbay and returns her to Neo Roanoke.
- To get a hold of Orb's mass driver, the Earth Alliance demands Orb to concede with them or be attacked for siding with ZAFT. Murrue decides the Archangel will support Orb and its crew members are discharged if they no longer wish to fight. Muruta Azrael, leader of Blue Cosmos, attacks Orb with three new mobile suits, the Forbidden, Raider, and Calamity. When Kira starts to have trouble with them, Athrun in the Justice arrives to help.
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- The PLANT Supreme Council supports Chairman Durandal's new policy, while ZAFT military headquarters issues orders for the Minerva to destroy the Archangel. Shinn defeats Kira and destroys the Freedom. The Archangel is apparently destroyed.
- The Orb Union space colony, Heliopolis, is attacked by ZAFT, despite its neutrality since the beginning of the Bloody Valentine War. Kira Yamato accidentally sees the Earth Alliance's new prototype mobile suits, which have been secretly constructed at the Heliopolis Morgenroete factory. He encounters his childhood friend, Athrun Zala, now a ZAFT soldier as one of the attackers.
- The Minerva fights the joint forces of the Earth Alliance and Orb. The Archangel again intervenes and Kira and Athrun clash again with Athrun losing. Shinn decimates the Orb forces in his anger and is even able to destroy one of the stolen mobile suits, but he unknowingly kills Captain Todaka who once helped him.
- Retitled Phase 51. 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.
- The Minerva uses its Tannhauser cannon to destroy the large debris but hundreds of small pieces descend towards Earth and destroy cities while causing heavy damage and numerous casualties. Meanwhile, Shinn saves Athrun and they both land safely on the Minerva, which has entered the atmosphere. After the incident ZAFT provides aid to the damaged Earth, while the Minerva crew is informed about what the terrorists had said. The Minerva then heads towards Orb.
- Covers the events of Gundam SEED Destiny Phases 43 to 50 and "Final Plus".
- The Minerva must destroy a fixed positron cannon emplacement to break through to Gibraltar. Though hesitant at first after meeting Shinn, they are helped by a young resistance fighter named Coniel, who provides data of a secret tunnel that will lead near the positron cannon. The Minerva and the other ZAFT forces draw out the Earth Alliance mobile suits and mobile armor while Shinn heads through the tunnel and destroys the cannon.
- A recap episode explaining the events of the series and part of unexplained events in Orb from Gundam SEED, from Shinn Asuka's point of view.
- While gathering intelligence under the guise of a shopping trip at Copernicus City, Lacus receives a message from Meer, who is afraid of being killed. Though Athrun and Meyrin insists it is a trap, Lacus decides to meet Meer anyway. The would be assassins are killed, but Meer is mortally wounded.
- 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.
- Covers the events of Gundam SEED Phases 1 to 21.
- Covers the events of Gundam SEED Phases 22 to 40.
- Covers the events of Gundam SEED Phases 41 to 50.
- Chairman Durandal muses about how Kira and Lacus met and their relationship. The episode also shows parts of the Chairman's own relationship with Talia Gladys and his motives. This episode is largely composed of footage from Gundam SEED.
- The Archangel saves Kira as they enter the Earth's atmosphere. As a result, they land in ZAFT-controlled territory in the Sahara in northern Africa, far from their intended target, Alaska. Flay begins to take care of Kira and comforts him when he is tormented by the memories of the spacecraft that was destroyed in the previous battle.
- The Minerva leaves Orb but an Earth Alliance fleet awaits them right outside Orb territorial waters. The Minerva is forced to break through, since Orb will not let them return. The situation worsens when the Earth Alliance deploys its new prototype mobile armor, but thanks to Shinn's SEED factor, he causes heavy damage to the Earth Alliance's fleet, and ultimately, their retreat. Meanwhile, Athrun rejoins ZAFT.
- The Archangel, without Cagalli and Ledonir on board, leaves Orb territory for Alaska. The Zala Team, who is patiently waiting, engages them in a battle. Kira grounds the Duel, Buster, and Blitz with the help of Mu and Tolle, who is now the second Skygrasper pilot. As Kira and Athrun fight, Nicol intervenes, but he steps into Kira's fatal attack.
- The GENESIS, a huge gamma-ray laser wipes out a large portion of Earth Alliance's forces. The Earth Alliance forces are forced to withdraw temporarily to regroup. During the intermission, each of the couples on board the Archangel, Kusanagi, and Eternal prays of each others safety in the upcoming battle.
- A battle with ZAFT submarine forces led by Commander Marco Morassim prevents Kira from fighting alongside Mu and Cagalli in their FX-550 Skygraspers. Cagalli's Skygrasper sustains damage and is forced to turn back, but she encounters Athrun's transport plane; her Skygrasper is shot down, but not before shooting down his transport plane, forcing Athrun in his Aegis to eject from the transport plane. By chance, they are both stranded on the same deserted island.
- Retitled Phase 15.5. A recap of the first fifteen episodes of Gundam SEED Destiny.
- Kira and friends discuss matters about the PLANTs during the aftermath of the assassination attempt. During that time, they are informed that Cagalli will be marrying Yuna Roma Seiran. Kira decides to use the Freedom to abduct Cagalli from the ceremony, returning to the Archangel. Yuna orders Cagalli's immediate capture. Instead, Colonel Todaka salutes while letting the Archangel submerge into the ocean.
- 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.
- 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.
- A battle between the Lesseps and the Desert Dawn commences. Kira and the Desert Tiger fight a battle where they realize the pain of having an enemy who is not an abstraction. With the Strike's power almost depleted, Kira has no choice but to destroy Andrew's TMF/A-803 LaGOWE or die himself.
- 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.
- After being framed as a traitor, Athrun tries to escape in a ZGMF-2000 GOUF Ignited, taking Meyrin Hawke with him. They are pursued by Shinn , and Rey .
- 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. Kira awakes and finds himself in the care of Lacus.
- 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.
- The real Lacus on television states that there is someone who has the same face, voice and name as herself in the PLANTs. She also states that people should find out more about Chairman Durandal's actions before believing in his lies. Djibril arrives at the Daedalus Lunar Base, where he fires the Orbital All-Aspect Tactical Cannon, Requiem, at the PLANT capital, Aprilius. The attack on Aprilius fails, but Januarius One through Four is hit, and they collide into December Seven and Eight causing them to collapse also. The Minerva returns to space.
- 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.
- 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 war has ended, and at Malchio's orphanage in the Marshall Islands, Kira, Athrun, Lacus and Cagalli reflect on the past and discuss the future.
- 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.
- Though the Desert Tiger has spared the lives of civilians, Desert Dawn members brashly challenge the ZAFT forces, because of the devastation they caused. The attack ends in failure, but most are saved by Kira in the Strike.
- 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.
- After the battle at Dardanelles, the Minerva returns to base for repairs. Athrun temporarily leaves the Minerva to contact the Archangel with the help of freelance photographer Miriallia Haw. Meanwhile, Rey Za Burrel and Shinn are ordered on a recon mission of an abandoned Earth Alliance base nearby, and are disturbed by what they find.
- Two years after the First Bloody Valentine War, Cagalli Yula Athha and "Alex Dino" meet PLANT Chairman Gilbert Durandal at the new PLANT, Armory One, to discuss important matters. At the same time, three unknown individuals infiltrate Armory One and steal three new ZAFT mobile suits. They are confronted by pilot Shinn Asuka in the ZGMF-X56S Impulse.
- 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.
- After the attack on the PLANTs by the Requiem, the Orb forces begin their preparations to leave Earth. ZAFT begins their assault on Requiem and the Minerva is sent to the front lines. Lunamaria is given the task of destroying Requiem's controls while the Destiny, the Legend, and Minerva divert the enemy's attention away from her. The Destiny and the Impulse manage to destroy Requiem's controls. Djibril attempts an escape on the Girty Lue, but Rey discovers him and destroys the Girty Lue. Cagalli parts with the crew of the Archangel and watches the ship leave for the Moon.
- 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.
- 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.
- Lacus and Andy reunite with the crew of the Eternal while Miriallia rejoins the Archangel crew taking up her former position. Meanwhile the Minerva travels across the ocean on its way to deliver a sickly Stella to a ZAFT research facility, when they are ambushed by the joint forces of the Earth Alliance and Orb off the coast of Crete.
- The abandoned facility turns out to be the place that creates the Extended pilots. The truth about this creation and the bodies they find traumatizes every ZAFT personnel tasked with securing the facility. The three Phantom Pain pilots hear of ZAFT at the lost facility, causing Auel to snap, and Stella to go berserk in her mobile suit, and heads to the facility on her own in an attempt to "protect mother". Shinn, with the help of Athrun, takes down her machine.
- 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. The Minerva arrives at Station 1 and begins their assault on the Archangel and Eternal. Lunamaria sorties in the Impulse and when she goes to take out the Eternal Meyrin calls out to her to stop her. 'Lunamaria is shocked that Meyrin is still alive and that she is on board the Eternal. Meanwhile Athrun is reunited with Dearka and an angry Yzak who decide to help him destroy Station 1. In the aftermath, Kira and Athrun destroys Relay Station 1, and Terminal forces go to attack Requiem itself.
- 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.
- While the Minerva battles the Girty Lue, the Minerva pilots fight against the stolen ZAFT prototypes in the Debris Belt. Even though it looks bad for the ZAFT forces at first, they are able to overwhelm the enemy thanks to Athrun's plan.
- 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.
- ZAFT attacks Orb because Djibril was given sanctuary there. To help the country, Erica Simmons and Ledonir give Cagalli the golden mobile suit, ORB-01 Akatsuki, which was given to her by her father. Regaining the command of her country, Cagalli orders for Yuna to be arrested for treason and regroups the Orb forces. The battle turns in favour for Orb, so the Minervas pilots are ordered to deploy, but Shinn decides to deploy alone.
- Cagalli tries to prevent her country from joining the Earth Alliance but the Orb council, especially the Seiran family, is against her wish to stay neutral. In the PLANTs, Athrun meets Yzak and Dearka and remembers the past while ZAFT prepares to send troops to Earth. The Minerva is warned by Andrew Waltfeld that they should leave Orb at once, because the country will ally itself with the Earth Alliance soon.
- 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.
- 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.
- Meer visits the troops at Diocuia's port for a morale-building concert. The Minervas pilots are greeted by FAITH member Heine Westenfluss, who escorts them to Chairman Durandal. Durandal reveals ZAFT is fighting a war against the Logos, a secret organization who create wars for profit.
- 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.
- The Archangel, Eternal, and Kusanagi plunge into the battle, trying to keep both sides from using their weapons of mass destruction. Rau destroys Flay's escape shuttle, killing everyone on board. Flay's spirit visits the grief striken Kira to apologize and thank him. Kira destroys the Providence with the Freedom, while Athrun remote-destructs the Justice to destroy GENESIS. With both the PLANTs and the Earth Alliance forces in disarray, the renegade moderate faction of the PLANTs seize the opportunity to call for a cease-fire, effectively ending the war.
- 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 Archangel as well to continue protecting his friends. Duel Gundam is upgraded with an Assault Shroud.
- The Minerva arrives at the Mahamul base, and Captain Gladys discusses plans with commander Joachim Ruddle to fly through to Gibraltar. Athrun meets Shinn on the Minervas deck and they talk about the responsibility of having power.
- ZAFT soldiers loyal to Patrick Zala set Junius Seven on a collision course for Earth. Tensions rise between Cagalli and Shinn due to Shinn blaming the Athha family for his family's death. Meanwhile, Lord Djibril and Logos leaders decide to use the Junius Seven incident to destroy the PLANTs. While Yzak Joule and his squad plan to destroy Junius Seven's debris, they are confronted by GINN High Maneuver II units.
- Covers the events of Gundam SEED Destiny Phases 1 to 13.
- Le Creuset attacks once again as the Archangel and the 8th Fleet approaches Earth. The Archangel is able to descend to Earth, but not without the loss of the entire 8th Fleet. Yzak Joule, the pilot of the Duel, vents his frustration by destroying a spacecraft carrying Heliopolis refugees that Kira had rescued previously.
- 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.
- A three way battle between ZAFT, Phantom Pain, and the GINN High Maneuver II types, piloted by supporters of the late Patrick Zala, takes place at the debris of Junius Seven while it moves towards Earth. Athrun also helps in a ZAKU but is confronted with memories of his father when it turns out that the terrorists still believe in the path that Patrick Zala had chosen. Despite the efforts of the Joule Team and the Minerva crew, Junius Seven continues to move towards Earth.
- 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.
- 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.
- Athrun and Kira recall the past events from their perspective and explain why they follow the paths they have chosen.
- With everything that has happened, Kira becomes depressed. He is comforted by Lacus, who is strolling around the ship without permission. Kira returns Lacus to Athrun against orders, but refuses Athrun's invitation to change sides.
- The Earth Alliance blames the PLANTs for the fall of Junius Seven and orders the PLANTs to disarm while they secretly prepare for an attack. In response, the PLANTs prepares their defenses. A battle starts between the two forces which almost ends in the destruction of the PLANTs when the Earth Alliance uses their new GAT-04 Windams armed with nuclear weapons. However, thanks to a new weapon, the attack is thwarted. Meanwhile, Athrun meets Gilbert Durandal.
- Covers the events of Gundam SEED Destiny Phases 29 to 42.
- Chairman Durandal makes a speech, which is televised worldwide. Lord Djibril is greatly angered by the speech, which blames the Earth Alliance, Blue Cosmos and Logos for the attacks by the Destroy and starting another war. Meanwhile, the crew of the Archangel debates what to do with the captive Neo, who is physically identical to their fallen comrade, Mu La Flaga.
- Kira and Cagalli are sent into a nearby ZAFT controlled city to gather supplies with Natarle and the Desert Dawn. The two teenagers get caught in an attack by the Blue Cosmos, and when Kira saves a man who happens to be Andrew Waltfeld, they are invited to the ZAFT base. There, Andrew reveals that he knows Kira is the pilot of the Strike and a Coordinator, but lets them leave safely.
- Sven Cal Bayan and his team are sent to eliminate a Coordinator refugee camp suspected of harboring terrorists. Sven has flashbacks of his military training and conditioning when he was a child. Sven proceeds to massacre the camp without hesitation. In another battle, while defending the Earth Alliance Forces ground carrier, Bonaparte, Mudie Holcroft is killed while fighting ZAFT forces. Meanwhile in space, Selene tests the new AI piloted GSX-401FW Stargazer with its Voiture Lumiere propulsion system.
- A recap of the first 25 episodes. Narrated by Tony Sampson, Miguel Aiman's voice actor .
- 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.
- GENESIS' second attack cripples the Earth Alliance's reinforcements and destroys their Ptolemaeus lunar base. The Three Ships Alliance save the PLANTs from the second wave of nukes. Mu fights Rau in the ZGMF-X13A Providence while Kira and Athrun fight the Forbidden, Raider, and Calamity. On the Dominion, Natarle becomes fed up with Muruta and orders the crew to escape. Muruta fires at the Archangel , but Mu sacrifices himself to protect them. In revenge, the Archangel fires and destroys the Dominion.
- Rey and Shinn are arrested, but Chairman Durandal orders the charges dropped. Stella is given the GFAS-X1 Destroy mobile armor, and levels three cities, including Berlin.
- Athrun intervenes in the battle between Kira, Shinn, and Rey, which shocks Shinn who believed that he had killed Athrun previously. Yuna is crushed by a GOUF Ignited when he tried to escape while Djibril successfully escapes to the Moon aboard an orbital shuttle. With the ZAFT flagship destroyed, Captain Gladys takes command and orders a temporary retreat. After the battle, Cagalli broadcasts a global announcement about the war with Logos but she is interrupted by Meer, who is in turn interrupted by the real Lacus.
- ZAFT and their allies attack Heaven's Base, and despite their great numbers, their forces are weakened by the new Logos weapon Nibelung and five Destroy units. The situation changes when the three mobile suits of the Minerva launch and decimate the Logos forces. Djibril flees the base before its surrender.
- As the Minerva leaves Carpentaria, it is attacked by Phantom Pain. During the battle, Shinn discovers the construction of a hidden Earth Alliance base who are oppressing the local citizens. He destroys the base to free the citizens, killing the fleeing soldiers. Back on the Minerva, Athrun slaps Shinn and tells him to use his power more properly.
- Le Creuset launches an attack on the Archangel. Kira's desire to protect his friends awakens an unknown almost berserker ability. He single-handedly defeats the attacking Blitz, GAT-X103 Buster, and GAT-X102 Duel.
- Both the Minerva and Archangel try to stop the Destroy, but Shinn hesitates when Neo tells him that Stella is the pilot. Kira manages to blow up the Destroy, fatally wounding Stella and angering Shinn. Meanwhile, Captain Ramius encounters the defeated Neo.
- The world is thrown into chaos after the Break the World incident during the Second Bloody Valentine War. A ZGMF-1017 GINN attacks a city where DSSD members Selene McGriff and Edmond Du Clos are in and causes massive damage until it is stopped by a linear tank commanded by Edmond, who is mortally wounded in his attack. Meanwhile Selene and another DSSD member, Sol Ryuune L’ange, leave for space while Phantom Pain deploys its pilots to fight ZAFT mobile suits that attack an Earth Alliance base.
- Stella is brought aboard the Minerva for medical treatment, while the Archangel works at getting Lacus and Andrew Waltfeld back into space.
- The Dominion retreats so their pilots can get their medicine. Mu and Dearka enter the Mendel colony to confront Rau and Yzak. Kira comes to their aid and he and Mu are shocked to discover Rau has a few secrets to reveal.
- Cagalli is surprised to find Athrun on the same deserted island. She attacks him, but she is overpowered and captured. When everything settles down, the two discuss the war and the reason why they are fighting. At sunrise, they are rescued by their respective comrades.
- The battle at Armory One continues. Athrun helps Shinn in a ZAKU but fails to harm the three prototypes. Meanwhile, a Mirage Colloid cloaked ship attacks the colony, commanded by a mysterious masked man who pilots a new mobile armor.
- Athrun returns to the PLANTs on a shuttle to speak to his father, but he is arrested. Lacus and 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.
- Cagalli intervenes and orders the Orb forces to stand down. But Yuna orders the Orb forces to attack to begin a three way battle. Kira's interference agitates the other pilots as he disables mobile suits on both sides, making him the prime target of Heine and Stella. As Stella charges to attack the Freedom, she kills Heine in the process.
- Kira survives due to the Freedom's cockpit being intact, and is rescued by Cagalli. Durandal's words inspire a widespread popular uprising against Logos, while the damaged Archangel heads for Orb. Durandal visits the Minerva and introduces the Destiny and Legend mobile suits, which are intended as replacements for the Impulse and Saviour, respectively.
- The Zala Team make another effort to destroy the Archangel and the Strike. Dearka in the Buster is shot down by Mu and surrenders. Tolle attempts to aid Kira, but he is killed by Athrun. The grief Kira and Athrun suffer over their friends' death is enough for them to try to kill each other.
- Kira and Mu face terrifying revelations in an encounter with Rau. Dearka and Yzak have their own meeting where they question what they are truly fighting against. Meanwhile, the Dominion and the Earth Alliance once again attacks. Rau returns to his ship and sends Flay back to the Earth Forces.
- Shinn destroys Athrun's GOUF Ignited. Athrun and Meyrin, who are thought dead, survive. Ledonir Kisaka rescues them and brings them to the Archangel, which has returned to its underwater port for repairs.
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