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| - Two years after the First Alliance-PLANT War, Cagalli and "Alex Dino" (Athrun Zala pretending as Cagalli's bodyguard) meet PLANT Chairman Gilbert Durandal to discuss important matters. At the same time, three unknown individuals infiltrate the new PLANT Armory One and steal three new next-generation ZAFT mobile suits. They are however, confronted by elite pilot Shinn Asuka in the ZGMF-X56S Impulse.
* Phase 02 - Those Who Cry Out For Battle The battle at Armory One continues. Athrun helps Shinn in a ZAKU but fail 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.
* Phase 03 - Sign of Gunfire (Due to the 2004 Chuetsu Earthquake broadcast was interrupted) The new ZAFT battleship Minerva chases the Girty Lue. Meanwhile, Cagalli and Athrun are led through the ship by Durandal but when Cagalli holds a speech about power and then she is confronted by an angry Shinn. Then they find the enemy ship and the Minerva's mobile suits are ordered to launch.
* Phase 04 - Battlefield Of Stardust While the Minerva battles the Girty Lue, the Minerva pilots fight against the stolen ZAFT prototypes in the Debris Belt. Although at first it looks bad for the ZAFT forces, but they are able to overwhelm the enemy thanks to Athrun's plan.
* Phase 05 - Unhealable Scar ZAFT soldiers loyal to Patrick Zala set Junius Seven on a crash course for Earth. Tensions also rise between Cagalli and Shinn due to Shinn blaming the Athha family for his family's death. Meanwhile, Lord Djibril and Logos bigwigs 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.
* Phase 06 - When The World Ends A three way battle between ZAFT, the Phantom Pain and the GINN High Maneuver II types 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 tries of the Joule team and the Minerva crew, Junius Seven continues to move towards Earth.
* Phase 07 - The Dazed Earth The Minerva uses it's 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 entered the atmosphere. After the incident ZAFT provides help to the damaged Earth, while the Minerva crew is informed about what the terrorists said. The Minerva then heads towards Orb.
* Phase 08 - Junction The Minerva enters Orb where the ship is repaired and Talia meets with Maria Bernes AKA Murrue Ramius. Meanwhile, the Orb government considers an alliance with the Earth Alliance much to Cagalli's protest. Athrun meets up with Kira and Lacus and discusses with Kira what he witnessed in space and afterwards plans to go to PLANT. Shinn in the meantime visits a memorial at Orb and meets none other than Kira and Lacus.
* Phase 09 - Prideful Fangs The Earth Alliance blames PLANT for the fall of Junius Seven and orders PLANT to disarm while they secretly prepare for an attack, in response PLANT prepares for their defense. Finally a battle starts between the two forces which almost ends in the destruction of Aprilius One when the EA 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.
* Phase 10 - Curse of A Father Athrun talks with Gilbert Durandal about the attack on PLANT and what will happen now. Because the people at PLANT are outraged, a Lacus look-alike hired by Gilbert Durandal calms the people. Athrun finally decides to do something and Durandal shows him the new ZGMF-X23S Saviour and offers him to become it's pilot. Afterwards Athrun meets the fake Lacus again, Meer Campbell.
* Phase 11 - The Chosen Road 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 PLANT, Athrun meets up with Yzak and Dearka and remembers the past while ZAFT prepares to send troops to Earth. In the end, the Minerva is warned by Andrew Waltfeld that they should leave Orb because the country will ally itself with the Earth Alliance soon.
* Phase 12 - The Sea Dyed with Blood The Minerva leaves Orb but an Earth Alliance fleet awaits them right outside their waters. The ship is forced to break through them since Orb won't let them return. When the Alliance uses a new prototype mobile armor which can even withstand a positron blast and the situation worsens, but thanks to Shinn's SEED factor, he fights like a berserker which causes heavy damage to the Earth Alliance fleet, and ultimately, their retreat. Meanwhile, Athrun rejoins ZAFT.
* Phase 13 - Revived Wing While the Minerva crew praises Shinn for his incredible fight, Orb joins the Alliance much to Cagalli's dislike. Meanwhile, Kira and his friends are attacked by Coordinators who try to assassinate Lacus. When they use the new UMF/SSO-3 ASH mobile suits, Kira is forced to reactivate the Freedom to protect his friends. Although he disables all the enemy suits the assassins then self-destructs all of their suits.
* Phase 14 - Departure Towards Tomorrow Kira and friends discuss matters about PLANT during the aftermath of the assassination. During that time, they are informed that Cagalli will be married to 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.
* Phase 15 - Return to the Battlefield Athrun is reinstated to the ZAFT military and appointed to FAITH. He is given the Saviour mobile suit and assigned to the Minerva. Captain Gladis is also appointed to FAITH, which creates something of a conflict in the command structure; Athrun and herself now have more or less equal rank and strategic authority.
* Special Episode - Mobile Suit Gundam Seed Destiny -EDITED- (Recap) A recap of the last 15 episodes which informs about the political situation in the Earth sphere.
* Phase 16 - The Battle in the Indian Ocean As the Minerva leaves Carpentaria it is once again attack by Phantom Pain. A furious fight ignites between the two sides.
* Phase 17 - A Soldier's Qualifications
* Phase 18 - Assault on Lohengrin
* Phase 19 - Invisible Truth
* Phase 20 - PAST (Recap) A recap episode explaining the event so far happened in the series and part of unexplained events in Orb from Gundam SEED, from Shinn Asuka's point of view.
* Phase 21 - Roaming Eyes On a seemingly relaxing day, Shinn meets a girl named Stella who seems to have no past, who fell off a cliff while dancing. He jumps in the water to save her, also seeing she goes out of control from hearing the word "die". He assumes she suffered from trauma possibly from a war. They take shelter in a cave, because Stella can't swim, and they get to know each other, with Athrun rescuing them later on.
* Phase 22 - Sword From the Skies
* Phase 23 - Shadow of War
* Phase 24 - Passing Gazes After the battle at Dardanelles that resulted the Heine's death, the Minerva returns to base for repairs. Athrun Zala temporarily leaves the Minerva to contact Archangel and her crew, through the freelance photographer Miriallia Haw. Meanwhile, Rey Za Burrel and Shinn are tasked with a recon mission on an abandoned EAF base nearby, and in disturbed by the machines and facts that they have found. Towards the end of this episode, Rey was caught in shock after seeing the cloning machinery.
* Phase 25 - Place of Sins The abandoned facility turns out to be the factory that creates the extended pilots. The shocking truth about this creation, and the rotting stench of the bodies (revealed in the episode) is causing every ZAFT person tasked with securing the facility a trauma. On the other hand, the trio of Phantom Pain pilots got wind of the lost facility, and caused Auel to snap, and Stella to go berserk in her mobile suit, attempting to "protect the lost ones" in the facility. However, Shinn—with the help of Athrun—takes down her machine.
* Phase 26 - Promise Stella is brought aboard the Minerva for medical treatment, while the Archangel works at getting Lacus and Andrew Waltfeld back into space.
* Phase 27 - Unreachable Feelings Lacus and Andy reunite with the crew of the Eternal. Meanwhile the Minerva is travelling 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.
* Phase 28 - Remaining Life, Scattered Life The Minerva fights the joint forces of the Alliance and Orb. The Archangel again intervenes and Kira and Athrun clash again with bad consequences for Athrun. Meanwhile Shinn decimates the Orb forces in his anger and is even able to destroy one of the stolen mobile suits. In the end he unknowingly kills a person who once helped him.
* Phase 29 - FATES (Recap)
* Phase 30 - Instant Dream With the aid of Rey Za Burrell, Shinn takes the dying Stella from the Minerva's sickbay and returns her to Neo.
* Phase 31 - The Neverending Night Rey and Shinn are arrested, but Chairman Durandal orders the charges dropped. Stella is given the GFAS-X1 Destroy mobile armor, and levels 3 cities, including Berlin.
* Phase 32 - Stellar 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, Capt. Ramius encounters the defeated Neo, and receives a terrible shock.
* Phase 33 - The World Shown Chairman Durandal makes an emergency 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.
* Phase 34 - Nightmare The ZAFT High Council pledges its' support for Chairman Durandal's new policy, while ZAFT military HQ issues orders for the Minerva to destroy the Archangel. Shinn defeats Kira and destroys the Freedom.
* Phase 35 - Chaos Ahead Kira was able to escape the Freedom just in time, 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.
* Phase 36 - Athrun Escapes The episode title says it all. Athrun tries to escape in a ZGMF-2000 GOUF Ignited, taking Meyrin with him, but he is pursuded by Shinn (piloting the Destiny), and Rey (piloting the Legend).
* Phase 37 - Darkness of Thunder Shinn destroys Athrun's GOUF, but Athrun and Meyrin manage to escape. Ledonir Kisaka rescues them and brings them to the Archangel, which has returned to its' underwater port for repairs.
* Phase 38 - A New Flag 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. However the situation changes when the three mobile suits of the Minerva launch and decimate the LOGOS forces. In the end Djibril flees the base.
* Phase 39 - Kira of the Sky After the Eternal finds out about Durandal's true motives, they leave for Earth. However ZAFT discovers them and attacks. Kira helps them with the Strike Rouge and finally 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.
* Phase 40 - Golden Will ZAFT attacks Orb since Djibril hides there. Orb doesn't stand a chance against the enemy forces because of the incompetence of Yuna Roma Seiran. To help the country, Erica Simmons and Ledonir Kisaka give Cagalli the new mobile suit ORB-01 Akatsuki, which was created for her by her father. Under her command the Orb forces regroup and strike back. But then she attacks Shinn.
* Phase 41 - Refrain (Recap)
* Phase 42 - Freedom and Justice The Archangel arrives to help Orb against ZAFT. Shinn Asuka, piloting the Destiny overwhelms Cagalli Yula Athha, piloting the ORB-01 Akatsuki. Then Kira appears, piloting ZGMF-X20A Strike Freedom and helps push back the ZAFT forces.
* Phase 43 - Voice of Counterattack Athrun launches and rushes to lend aid to Kira, who is battling Rey and Shinn. At the same time, Yuna gets crushed by a GOUF Ignited as it is defeated, when he tried to escape form his Orb escorts. Djibril manages to escape to the moon and as the ZAFT flagship is destroyed, the Minerva takes over and orders for a temperory retreat. After that battle, Cagalli broadcasts a message to Chairman Durandal. She is interrupted by Meer, who is then interrupted by the real Lacus.
* Phase 44 - The Two Lacus The real Lacus says that there is someone who has the same face, voice and name as herself in the PLANTs. She also says that people should know more about Chairman Durandal, causing confusion over the world. After that, Chairman Durandal had was seen boarding a shuttle. Djibril is at the new Daedalus lunar base, which the Orbital All-Aspect Tactical Cannon, Requiem is located. When it is fired, it destroyed 6 PLANT colonies. It caused an uproar.
* Phase 45 - Prelude to Reform
* Phase 46 - The Song of Truth
* Phase 47 - Meer Although Meer was killed protecting Lacus, her story lives on. Athrun, Kira, Lacus and Meyrin read the diary of Meer Campbell. Athrun laments at the loss of Meer, stating that if he had not consented to her existence none of this would have happened. Lacus swears to remember Meer and avenge her sacrifice.
* Phase 48 - To A New World 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 Orb Union and the Kingdom of Scandinavia explicitly reject this plan. ZAFT repairs Requiem and fires it at the Alliance lunar base of Arzachel, killing the president of the Atlantic Federation. Terminal forces head towards Relay Station 1 of Requiem.
* Phase 49 - Rey Shinn and Rey are transferred to Messiah. Shinn is confronted by Durandal and Rey. Through a difficult mind struggle, Shinn finally decides to follow the course of action pointed out by Durandal and Rey. Meanwhile, Kira and Athrun destroy Relay Station 1, and Terminal forces go to attack Requiem itself.
* Phase 50 - The Final Power Kira is confronted by Rey, who, like Rau Le Creuset, is hellbent on the destruction of Kira. However, Kira temporarily stuns him by saying that his life is his own and he does not need to be someone else. Kira then proceeds to severely cripple the Legend in one blow. Athrun, meanwhile, faces Impulse and Lunamaria, which he defeats with ease. However, Shinn comes to Luna's rescue and enters SEED mode against Athrun however he is also defeated by Athrun in SEED mode, Requiem is destroyed in a joint effort of Akatsuki and Justice.
* Final Plus - The Chosen Future (replaces Phase 50, also known as an OVA episode.) 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.
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