In space, Athrun and Nicol launch in a Laurasia class ship’s re-entry capsule and head for Earth. After leaving the African continent, the Archangel enters the Red Sea and battles ZAFT’s amphibious mobile suits. At the same time, Patrick Zala takes Siegel Clyne’s place as leader of the PLANT Supreme Council. While patrolling in the Sky Grasper, Cagalli encounters a ZAFT transport plane and attacks it. The Sky Grasper is damaged, and the Aegis Gundam launches from the transport plane before it explodes. Cagalli crashes on a nearby island and runs into Athrun. She shoots him in his right arm, but he manages to disable her. As he is about to kill her with his knife, he stops when he realizes she is a girl. He then binds her hands and feet with ropes, and she tries to escape and falls into a stream. She then washes herself down in the rain to get rid of crabs in her clothes. Athrun then sits calmly while Cagalli’s clothes dry over a fire. He warns her that if she tries to take his gun he will kill her. She blames him for what happened at Heliopolis, and he tells her it wasn’t supposed to be that way. When he falls asleep, Cagalli steals his gun and says she doesn’t want people on Earth to die because of the Aegis Gundam. Cagalli tosses the gun aside as Athrun jumps her. Later, Athrun, Yzak, Dearka and Nicol attack the Archangel over the sea as it approaches Orb’s territory. As the heavily damaged Archangel approaches Orb, a fleet of Orb’s Aegis class destroyers attempt to block their entry. Cagalli calls the fleet and identifies herself as the daughter of Uzumi Nara Athha. The Aegis ships then fire at the Archangel and block Athrun from attacking.
Uzumi meets with his council and promises that he will deal with the Archangel. He then meets with Murrue, Natarle and Mu and says that Orb’s official story is that the Archangel was chased away. He explains that he wants the Strike Gundam‘s combat data, as well as information from Kira. Repairs begin on the Archangel, and Kira takes the Strike Gundam to Morgenroete’s facility. In his office, Uzumi meets with Kira’s parents Haruma and Caridad. Caridad says that they both promised not to allow the children to meet, and Uzumi says that fate intervened. At Morgenroete, Kira meets mobile suit designer Erica Simmons and is surprised to find an army of mass produced M1 Astray units. Erica tells him that she wants his help in creating an OS for Naturals to use mobile suits. Elsewhere, Athrun and the others infiltrate Orb to find the Archangel. He and Nicol search the city streets and are amazed by how peaceful everything is. While Kira works on the Strike Gundam’s OS, he thinks about his break up with Flay. Birdy flies outside, and Kira chases after it. Outside, Athrun and the others plan their next move when Birdy lands on Athrun’s wrist. He sees Kira run out of the factory and walks over to a fence dividing them. He gives Birdy back, and Kira tells him that it was a gift from an important friend. With repairs completed, the Archangel leaves Orb’s territory. Murdoch asks Kira why he’s ready for battle, and he says that they will be attacked as soon as they leave Orb. Sure enough, once the Archangel is alone, Athrun and the others attack.
The Archangel deploys a smokescreen, and Kira attacks with the Launcher Strike Gundam. He uses the Agni cannon to destroy Dearka and Yzak’s Guul sub-flight units. He then receives the Aile pack from the Sky Grasper and goes after Athrun and Nicol. He slices the Blitz Gundam‘s right arm off with his beam saber and knocks it away. He then attacks Athrun, who lands on a small island. Kira lands nearby after receiving the Sword pack and asks Athrun to retreat. Athrun asks Kira to shoot him because Kira promised he would. Nicol appears from nearby and tries to attack Kira. Kira swings the Schwert Gewehr like a bat and slices into the Blitz Gundam’s torso. Nicol asks Athrun to escape, just before the Blitz Gundam explodes. The crew congratulates Kira for destroying a Gundam, and Mu explains to a distraught Kira that they are soldiers, not murderers. In the next battle, Athrun relentlessly attacks Kira. Mu attacks Dearka with the Launcher Grasper, and both damage each other considerably. Mu crashes in the water, and Dearka crashes on a small island and surrenders when the Archangel targets him. Kira and Athrun continue to attack each other, and Tolle attacks the Aegis Gundam with the Sky Grasper. Athrun tosses his shield at the Sky Grasper, smashing the cockpit and beheading Tolle. Kira and Athrun both go into SEED mode and slice their suits apart. Athrun transforms and grapples the Strike Gundam. He sets the self destruct sequence and escapes before the Aegis Gundam explodes. After the Archangel leaves, Cagalli and Kisaka fly out to the island and find the ruins of the Aegis Gundam and the mostly intact Aile Strike Gundam, minus Kira. Athrun wakes up in an Orb plane and finds Cagalli pointing a gun at him. She asks him about Kira, and he tells her he killed his own friend.
On the Archangel, Kuzzey tells Flay that Kira is MIA. She presses him for more information, and he says that Kira is probably dead. A ZAFT plane arrives to pick up Athrun, and Cagalli gives him her necklace to protect him. Soon after, the Archangel finally arrives at the JOSH-A Alaska base. Several high-ranking officers review Kira’s file and comment that they can’t have Coordinator children piloting their new Gundams. Kira wakes up on a PLANT and finds Lacus and blind missionary Malchio watching over him. At the Alaska base, Natarle, Flay and Mu are transferred off the Archangel. Murrue asks Natarle to take care of Flay and hopes they can meet again. Across space and Earth, ZAFT forces prepare for the start of Operation Spit Break. Patrick announces the start of Spit Break and changes the target from Panama to Alaska. Every model of ZAFT mobile suit converges on Alaska to assault the JOSH-A base. Council member Eileen Canaver calls Siegel to tell him that Patrick lied to them and intends to attack Alaska. As the attack begins, Rau flies into the base through a secret entrance with information provided by Murata Azrael. Mu finds Rau in an empty control room, and the two shoot at each other. Mu looks at a computer screen and sees that the Alliance is planning to use the Cyclops System. In a nearby hallway, Rau captures Flay and takes her with him. On the PLANT, Kira cries and tells Lacus he has to go back to Earth. She asks him if he’s going to fight ZAFT again, and he tells her he doesn’t want to fight ZAFT or the Alliance. She then asks him to come with her and has him put on a red ZAFT elite pilot uniform. She takes him to a secret hangar and shows him the new Freedom Gundam. Kira asks her why she’s giving it to him, and she tells him he needs its power to make what he wants happen. Kira steals the Freedom Gundam and disables two GINNs as they attack him. He then flies by Athrun’s shuttle as he heads for Earth.
The ZAFT forces continue their assault on JOSH-A and destroy the defending units. The Archangel is damaged during the assault, and Mu lands a Spearhead fighter inside one of the ship’s launch bays. He informs Murrue that the brass have abandoned JOSH-A and have equipped the base with a Cyclops System, which will destroy everything within 10 kilometers. Their plan is to draw in as many ZAFT forces as possible and destroy them with the Cyclops System. Miriallia asks if they’re just supposed to throw their lives away because the brass planned to sacrifice them to destroy ZAFT. Murrue decides to retreat from the battlefield and orders that a message be sent to the surrounding ships to escape. A group of GINNs attacks the ship, and one pulls up in front of the bridge and prepares to fire. At the last second, Kira attacks from above with his beam rifle and disables the GINN. He tells Murrue to escape while he provides cover, and she informs him about the Cyclops System. Kira fires all of his weapons and disables scores of ZAFT mobile suits. He then broadcasts a message on an open frequency to tell ZAFT and the Alliance to escape. Yzak says that he won’t fall for that trick and attacks Kira. He locks fists with Kira and fires his shoulder cannon, but Kira dodges. Kira moves in to make a killing blow with his beam saber, but at the last second he slices off the Duel Gundam‘s legs and kicks Yzak away. The Cyclops System activates, and soldiers caught within the base begin to explode as everything is destroyed. As the shockwave spreads, Kira saves a damaged GINN and takes it to safety. Afterwards, Kira says that a lot of things happen. Mu asks him if he was at ZAFT, and Kira answers that he was, but he adds that he’s not with ZAFT or the Alliance. Athrun returns to Aprilius One to find everything in disarray. Commander Ray Yuki tells Athrun that Operation Spit Break was a total failure and that most of the attacking forces were destroyed. On top of that, he says that apparently Lacus helped someone steal a top secret new mobile suit. Athrun walks into Patrick’s office and hears him handing out orders to other officers. He says he can’t believe Lacus would help a spy, but Patrick shows him a surveillance video of Lacus in the Freedom Gundam’s hangar. He tells Athrun that Lacus is no longer his fiancé and that she’s been charged with treason. He orders Athrun to take the Justice Gundam and use it to track down the Freedom Gundam. His orders are to kill the pilot and anyone who has come into contact with the suit, and if he can’t recover it, to destroy it. Athrun asks why he has to go to those lengths, and Patrick explains that the Justice and Freedom Gundams are equipped with an Neutron Jammer Canceler.
Athrun visits Lacus’ home, which has been ransacked by ZAFT forces searching for her. The pink Haro jumps out of the bushes, and Athrun goes to a ruined theater where he finds Lacus singing. He asks her if she really helped a spy, and she tells him that all she did was help Kira. He points his gun at her and says that’s impossible because Kira is dead. Lacus tells him it’s true because Malchio found him and brought him to her. Lacus asks Athrun what he’s fighting for. She tells him that if it’s for medals or his father’s orders, she and Kira will become his enemies. On Earth, the Archangel arrives at Orb. Cagalli boards the ship and knocks Kira to the ground because she’s so relieved to see he’s alive. Athrun considers Lacus’ words and heads for Earth in the Justice Gundam. On Earth, a ZAFT fleet attacks the Alliance’s Panama base. A ZAFT commander questions the decision, and Rau tells him they have to retaliate and break the Alliance’s momentum. Yzak leads the ZAFT mobile suit forces in the attack, and the Alliance unleashes its first mass production mobile suit, the Strike Dagger. ZAFT drops the Gungnir System from space, which sends out an EMP (electromagnetic pulse). The EMP wave disables the Strike Daggers and destroys the mass driver. Alliance soldiers surrender, but ZAFT pilots ruthlessly execute them as revenge for Alaska. Flay pulls a gun on Rau, and he tells her that if she shoots him, soldiers will kill her. He tells her she could commit suicide instead, and she surrenders. Blue Cosmos leader Multa Azrael meets with several men to discuss the current situation. Now that Panama’s mass driver has been destroyed, they have no way of sending supplies to the Moon base. Orb refuses to help them, and Azrael says they shouldn’t let Orb hide behind the excuse of neutrality. He says he’ll handle negotiations, but he’s also eager to test his three new Gundams. The Atlantic Federation sends an ultimatum to Orb: help the Alliance or be branded a ZAFT supporter. Murrue addresses the crew and informs them that the Alliance is planning to attack Orb. She says she can’t give them orders anymore, and that anyone who wants to leave the ship should do so. Athrun returns to the Marshall Islands and finds several children playing near the wreckage of the Justice Gundam with Malchio. Miriallia goes down to the brig and sets Dearka free. He remembers her and Flay trying to kill him, and he tells her he didn’t kill Tolle. He asks what’s going on, and she says the Archangel is going into battle and that she plans to fight because Orb is her homeland.
Uzumi sends a response to Azrael stating that Orb is rejecting the ultimatum. Athrun and Malchio watch a news broadcast that says the Alliance will attack Orb. Murrue asks Mu why he came back to the ship at Alaska, and he responds by kissing her. She says she doesn’t like mobile armor pilots, and he says that he’s a mobile suit pilot now and kisses her again. The Alliance fleet begins its attack and deploys its Spearhead and Strike Dagger forces. Kira launches in the Freedom Gundam, followed by Mu in the repaired Aile Strike. On the carrier Powell, Shani Andras launches in the Forbidden Gundam, followed by Clotho Buer in the Raider Gundam and Orga Sabnak in the Calamity Gundam. Orga attacks the M1 Astray forces on the ground, while Shani and Clotho attack Kira and the Archangel. Several Spearheads attack the Archangel, but Dearka destroys them and tells the ship to escape. Athrun flies over the battlefield and sees Kira fighting the three Gundams. Clotho fires his mouth cannon at Kira, and Athrun steps in and blocks the shot. Kira asks Athrun if ZAFT is participating in the battle, and Athrun says he’s doing it on his own. Athrun attacks Clotho while Kira engages Shani and Orga randomly shoots from the ground. The three pilots suddenly panic when their drugs wear off, and they retreat from the battle. Kira thanks Athrun for his help and asks him what his intentions are. Athrun answers that he was sent to capture or destroy the Freedom Gundam, but he has no intention of doing that. The two land and greet each other in person, and Cagalli runs over to them. Afterwards, Uzumi tells Murrue that the Archangel has to head for space because Orb will be conquered soon. He says the world will be torn apart by the ideals of Patrick and Azrael, and that they should fight to end the conflict. Dearka asks Athrun if they should go back to Carpentaria. Athrun says he fought and followed orders because he wanted to end the war, but he doesn’t know now what he should be fighting for. Kira tells him he should come along so that they can search for the answer together. The Archangel is fitted with a space booster, and Azrael sends the three Gundams to attack again. The Archangel takes off and fires its Lohengrins to provide power for the booster. Uzumi drags Cagalli to the Kusanagi and gives her a picture of her as a baby with her brother Kira. As the Kusanagi speeds across the Kaguya mass driver, Kira and Athrun fight off the three Gundams. At the last minute, Kira and Athrun grab onto the Kusanagi as it takes off. Uzumi then activates a self-destruct program that completely destroys the Kaguya mass driver and kills him.
This installment of the Special Edition loosely covers episodes 24-40. Kira’s battles with Marco Morassim are reduced to a few frames, and the editing in this part is some of the roughest so far. There are literally only a few seconds separating Nicol’s death from the next brutal battle between Kira and Athrun. There’s also only a few seconds separating Athrun and Cagalli on the island from the next battle. The pacing gets a bit better during the Alaska portion of the story, but a lot of the stuff after that is also cut. Athrun meets with Lacus as in the TV version, but they removed the part where gunmen attempt to assassinate her. The special ends with the Orb arc, which is quite interesting and unfortunately cut very short. Had this special been longer, more of that arc could have been shown. Other important events could’ve also been shown in their proper context, instead of as quick flashbacks spread around here and there. Overall it’s a decent production, but it’s not edited well enough for newcomers who haven’t seen the TV series to understand it.