In Orb, Cagalli and Yuna ride in a procession to their wedding. Down in the Archangel‘s hangar, Murrue asks Kira if he’s sure about what he wants to do, and he answers that he isn’t, but he knows doing nothing would be worse. With its crew aboard, the Archangel launches from its underwater hangar and takes to the skies so that Kira can deploy in the Freedom Gundam. Just as Cagalli and Yuna begin to exchange their vows, Kira arrives and disables all the M1 Astrays assigned to guard the wedding. Yuna cowers behind Cagalli, and Kira grabs her and flies away. He returns to the Archangel, which escapes underwater. Todaka has his fleet do nothing because he hopes the Archangel can take care of Cagalli. Durandal is informed that the Minerva reached the Carpentaria base after fighting an Alliance fleet, during which time Shinn personally destroyed six ships. Durandal concludes that Shinn’s SEED factor has awakened, and he wonders if Shinn will be able to defeat Kira. At Carpentaria, Athrun arrives with the Saviour Gundam and reports to the Minerva for duty. Shinn is surprised to see him and wonders why he’s in FAITH now. Athrun rides in an elevator with Lunamaria, who tell him about the battle with the Alliance and Cagalli’s marriage. Athrun reports to Talia and gives her a FAITH badge from Durandal. Examining the current situation after the emergence of the World Security Treaty Organization, Talia concludes that Durandal wants them to go to the Suez area. The Minerva launches and eventually encounters an Alliance force consisting of 30 Windams and the Chaos Gundam. Talia asks Athrun what he plans to do since she can’t give him orders, but he decides to launch and agrees to command the mobile suit team. After launching, Athrun takes on Sting, while Shinn attacks the Windams and Neo. Shinn easily destroys several Windams, but Neo evades his attacks by hiding in the clouds and firing back under their cover. Several Windams gang up on the Force Impulse, while the rest attack the Minerva. Auel approaches from underwater and attacks the ZAFT sub Nyiragongo, which is accompanying the Minerva. Shinn chases after Neo, but Stella attacks him and knocks him into the ocean. Athrun attacks Neo, and Sting swings around to get behind Athrun. Athrun tells Shinn to retreat, but Shinn ignores him and fights the Gaia Gundam. Rey and Lunamaria fight Auel underwater, but they have trouble hitting him. Shinn comes across a new Alliance base and sees soldiers shoot civilian laborers who are attempting to escape. Neo orders everyone to retreat, and Auel destroys the Nyiragongo. Shinn destroys the Alliance base and smashes the fences separating the laborers from their families.
Back in the Minerva‘s hangar, Athrun slaps Shinn, and Shinn says he didn’t do anything wrong by saving those people. Athrun slaps him again and tells him that war isn’t about being a hero. Shinn says that Athrun doesn’t even know what he’s talking about and asks how he can accept a guy who was just recently an Orb bodyguard and is now back with ZAFT and in FAITH. Athrun grabs Shinn by the collar and tells him that once he has power, he’ll be the one who makes others suffer. Later, the Minerva attacks the Alliance’s Gulnahan base, and Shinn destroys the Lohengrin Gate while Athrun destroys the Gells-Ghe mobile armor. The Minerva later docks at the Black Sea port of Diocuia, where Talia and the pilots meet with Durandal and Heine. Talia asks about the situation in space, and Durandal tells her that there have been some small scale battles. She asks if there have been any motions for a cease fire, but he says the Alliance isn’t backing down at all. Shinn says that it’s important to avoid fighting, but there’s no choice when you’re threatened by an enemy. Athrun recalls Cagalli’s quote about the uselessness of retaliatory killings, and he says he didn’t know the answer to that question back then or now. Durandal says that people have always protested against war, and Rey adds that there are those who profit from war. Durandal says that the Logos organization is behind the war and reveals that they created Blue Cosmos. He wants to do something about Logos, but he knows that’ll be difficult. Later, Durandal asks Athrun if he knows where the Archangel went after leaving Orb, but Athrun doesn’t know. Durandal wants their help, and he figures that they have the real Lacus with them. Shinn takes shore leave and drives his motorcycle to a cliff overlooking the ocean. He sees Stella dancing on another cliff, and when she falls into the water, he jumps in and rescues her. He asks her if she wanted to die by being out there and not knowing how to swim, and she panics when she hears the block word “die.” After struggling with Stella, Shinn calms her down by reassuring her that she won’t die because he’ll protect her. As their clothes dry, Shinn talks to Stella and learns that she doesn’t know her parents. He sends out an emergency signal, and Lunamaria comes to pick them up on a boat. Sting and Auel search for Stella on the cliff, and they drive her up there. Shinn says goodbye and tells Stella that they’re sure to meet again.
Later, Heine, a FAITH member, is transferred to the Minerva and reports for duty. Elsewhere, Djibril berates Atlantic Federation President Joseph Copland for losing control of the war situation and allowing revolts to break out in Eurasia. Copland asks Djibril what he intends to do, and Djibril decides to call on Orb to send a fleet to the Black Sea and fight ZAFT. Stella wakes up after having her memories erased and wonders about the cloth that Shinn tied to her ankle. Talia briefs Arthur, Athrun and Heine on the situation and concludes that the Orb fleet is probably coming their way to reopen the Suez supply route. The next morning, the Minerva departs from Diocuia and heads for the Dardanelles. Heine speaks with Athrun from an observation deck and guesses that Athrun doesn’t want to fight against Orb. Athrun says he doesn’t, and Heine agrees that he doesn’t want to fight anyone either. But he adds that they’re soldiers in a war, and if they hesitate, they die. In an elevator, Athrun tells Shinn that the Orb/Alliance treaty would’ve never happened if Cagalli were there. He says she has a long way to go as a ruler, but she’s true to her feelings. Shinn think’s that’s garbage and that one can’t run a country with feelings. Athrun asks Shinn if he liked Orb and hates them only because his family was killed at Onogoro. The Orb fleet launches its M1 Astray Shrikes and Murasames, while its ships open fire on the Minerva. Shinn and Athrun take on the attacking mobile suits in the air. Talia orders Arthur to move the ship into position to fire the Tannhauser at the Orb fleet and Alliance carrier. Just before the Tannhauser fires, it’s destroyed by a shot from above from the Freedom Gundam. The Archangel appears behind Kira, and Cagalli launches in the Aile Strike Rouge. Cagalli identifies herself as the Orb representative and orders the Orb fleet to retreat. An angry Neo calls Yuna and demands to know what’s going on. He asks if that really is Cagalli and says that if he doesn’t get an immediate explanation, it will put Orb in an unpleasant situation. Yuna tells Neo that it’s an impostor and orders Todaka to attack the Aile Strike Rouge and Archangel. Todaka objects, and Yuna tells him that if they don’t attack, the Alliance will attack their fleet, and then Orb. The Orb ships fire a volley of missiles at Cagalli, but Kira destroys them all. Sting, Auel and a squad of Windams launch from the carrier John Paul Jones and head toward the Minerva. Shinn attacks Sting and the Windams, while Stella shoots at Athrun from the deck of the John Paul Jones. Heine launches in his GOUF Ignited, while Rey and Lunamaria stay on deck to defend the ship. Cagalli repeats her demand that the Orb forces retreat, but Kira tells her it isn’t going to work. Kira tells Cagalli to fall back and goes into SEED mode to disable the Orb and Alliance suits. On a nearby island, Heine fights Stella and destroys her beam rifle. Athrun and Shinn continue to fight Sting and Auel.
Kira comes under attack from several Windams and disables them. He then cuts off the Force Impulse’s right forearm and damages the Abyss Gundam‘s thrusters. Stella attempts to attack Kira, but he slices off her hands and knocks her away. Athrun attempts to call Kira and ask him what he’s doing, but there’s too much interference. Heine is furious that Kira is randomly attacking everyone and opens fire on him. Stella jumps up to attack Kira in quadruped mode with her beam blades, but she ends up slicing Heine in half when he gets in the way. Kira kicks Stella away, and the Orb fleet fires its retreat signal. The Minerva docks at the port of Turkios in the Sea of Marmara to offload its casualties and have the Tannhauser repaired. Heine’s personal effects are taken away, and Shinn says that if the Freedom Gundam and the Archangel hadn’t intervened, Heine wouldn’t have died. He thinks that their attempt to stop the battle was stupid. Athrun thinks to himself that he never expected Kira to get involved, and he decides to track him down before he does something stupid again. After speaking with Talia, Athrun launches in the Saviour Gundam to find Kira. In the Archangel‘s hot springs, Cagalli tells Lacus that she wonders if she did the right thing. Lacus answers that the only way to do anything is to make a decision and act on it. As Athrun drives through a city, he encounter Miriallia Haw. Shinn and Rey launch from the Minerva, and when Shinn asks why they’re on a recon mission, Rey explains it’s an order directly from headquarters. Kira and Cagalli come to the surface to meet with Miriallia, who explains to them that Athrun returned to ZAFT. Athrun then arrives in the Saviour Gundam, which Kira recognizes from the previous battle. Cagalli asks Athrun what he’s doing with ZAFT again, but unbeknownst to any of them, Lunamaria is eavesdropping. Athrun answers that he thought going back to ZAFT would be good for Orb, but Cagalli doesn’t buy it. Athrun asks Kira why he interfered and says that his appearance caused chaos and many unnecessary deaths. Cagalli says that they were just trying to prevent ZAFT from attacking Orb, and Athrun asks if she really thought just showing up would make Orb back down. He says that the war is the Alliance’s fault and that the PLANTs are trying to quickly end the fighting. Kira asks about Meer and mentions that the real Lacus was nearly assassinated by Coordinators. Kira says that until he finds out who was behind the attempt, he can’t trust the PLANTs. Shinn and Rey arrive at their target, an abandoned compound, and begin exploring on foot. Inside, they find tubes filled with bodies, which causes Rey to have a panic attack. Athrun thinks that Kira is jumping to conclusions and tells him to go back to Orb. Kira asks Athrun if he’ll fight Orb again, and Athrun says there’s no choice because they have to stop the Alliance. Kira says he doesn’t want to fight, and Athrun tells him to go back to Orb and leaves.
The Minerva arrives at the Alliance compound and deploys investigation teams. At the Suez base, a soldier informs Neo that the Lodonia lab wasn’t destroyed and has been discovered by ZAFT, which Stella overhears. She asks Sting and Auel what the Lodonia lab is, and Auel explains that it’s where they were before. Inside the lab, Talia, Arthur, Shinn and Athrun find many corpses of children and scientists. In a room filled with brains, Talia finds a computer and reads up on the Alliance’s Extended program, which created living weapons by experimenting on children with drugs and other methods. Athrun sees the file and recognizes the Raider Gundam. Auel begins to panic when he says his own block word, “mother,” and sets off Stella when he mentions her block word, “die.” Stella then steals the Gaia Gundam and heads to Lodonia. As she approaches, Shinn and Athrun take off and attack. Athrun causes some damage with his cannons, and Shinn slices open the Gaia Gundam’s cockpit and knocks it to the ground. When he zooms in on the open cockpit, he’s shocked to see Stella as the pilot. He grabs the injured Stella and takes her back to the ship. He pleads with the doctor to treat Stella, but the doctor tells him he can’t treat an enemy soldier without Talia’s permission. Shinn says that she might die, and she panics and attacks him and a nurse. Shinn gets her off the nurse, and Talia rushes in with several armed guards. After Stella is restrained, the doctor examines her and reports to Talia that Stella is an Extended. Stella wakes up and attempts to break out of her restraints, and when Shinn fails to calm her down, the doctor tranquilizes her. Later, she wakes up and does recognize Shinn. On the Archangel, Lacus decides to go to space over Kira’s objections. She says that she needs to find out what’s going on in space. Kira wants to go with him, but she tells him he has to protect Cagalli and the ship. At the Gibraltar base, Lacus impersonates herself and takes off in a shuttle with Andy. When Meer arrives, her manager says that Lacus is a fake. A squad of BABIs take off and fire at the shuttle, but Kira blocks the shots. He then disables the BABIs and flies alongside the shuttle for a while before breaking off.
Djibril speaks with Neo on video and is angry with him over his past failures. He says that the Minerva is being hailed as a champion of justice, and he wants Neo to destroy it once and for all this time. After the Minerva sets sail and approaches Crete, it’s picked up by a recon Murasame, and the Orb fleet goes into battle alert. The Minerva also goes into battle alert, but the Orb fleet opens fire first. More Orb ships appear near the Minerva, and Sting and Auel launch from the John Paul Jones. Shinn launches in the Core Splendor and forms up to the Blast Impulse Gundam, followed by Athrun in the Saviour Gundam. Shinn and Athrun fight with Auel and Sting, while Rey and Lunamaria stay on deck to intercept missiles and the Murasames. Talia sees that the fleet is trying to force them near Crete, but if they turn direction, they’ll be attacked by the other fleet. Auel uses the water as cover to fire on Shinn and run. Several Murasames join Sting in attacking Athrun, putting him on the defensive. A Murasame fires several missiles at the Minerva, damaging the ship and Rey’s ZAKU Phantom. It then tries to fire at the bridge, but its beam rifle is destroyed by the Freedom Gundam. Cagalli launches in the Aile Strike Rouge and again orders the Orb fleet to retreat. The Archangel fires its cannons into the water near the Orb ships, shaking them up. Cagalli addresses the Takemikazuchi and asks what’s the point of having a military if they can’t protect their ideals. Angered by Cagalli’s words, Shinn fires missiles at her, but Kira destroys them with his vulcans. He then attacks Shinn, who goes into SEED mode and dodges. Athrun attacks Kira and tells him to go back to Orb because he’s only bringing confusion to the battlefield. Sting attempts to attack the both of them, but Kira slices off the Chaos Gundam’s arms and weapons pods. Auel opens fire on Shinn, who ejects the Blast Silhouette and lets it take the damage. In the midst of the explosion, he tosses his beam javelin at the Abyss Gundam, killing Auel. Shinn calls for a Force Silhouette pack, and several Murasames begin an attack run on the Minerva, but Cagalli blocks their path and says ZAFT isn’t Orb’s enemy. The Murasame pilot, Baba, tells Cagalli that they’re following the orders of the current leader of Orb, whether they like it or not. He tells her to fall back and tosses the Strike Rouge out of the way. The Murasames open fire, damaging Lunamaria’s Gunner ZAKU Warrior and injuring her. Shinn destroys several of the Murasames, but Baba breaks through and performs a kamikaze attack on the ship. With the Minerva heavily damaged, Shinn switches to the Sword Silhouette. Shinn uses his anti-ship swords to attack the Orb fleet. Kira tells Athrun that he’s attacking what Cagalli wants to protect, so he goes into SEED mode and slices off the Saviour Gundam’s appendages. The Takemikazuchi moves forward and comes under heavy fire from the Minerva, and Todaka forces Yuna to abandon ship. Amagi and several other officers want to stay, but Todaka tells them to go to the Archangel. As the ship sinks, Shinn lands on the deck and slices apart the bridge, killing Todaka.
The second DESTINY Special Edition picks up right after the first and covers episodes 14-28. Basically, that’s mostly everything between Cagalli’s wedding to the second battle between the Minerva and the Orb fleet. Unlike the first SE, the editing here is much smoother. This version also cuts out a lot of the boring fat, including the overlong conversation between Kira and Athrun, as well as Lacus’ trip to space. Unfortunately, the Gulnahan battle is also cut down, which is a shame because it was personally one of my favorite episodes. Also lost is Andy fighting with his custom Murasame, so he effectively doesn’t appear at all. As far as new material, there’s a scene where Durandal considers Shinn’s battle record and his SEED factor. This should’ve been in the TV series, which failed to give any further explanation of what the SEED factor is, or why certain people have it. In addition, all traces of Lunamaria having a crush on Athrun are removed. She’s also substituted for Athrun when the boat comes to rescue Shinn and Stella.