In space, the Kusanagi‘s various components dock to form a complete battleship. Cagalli shows the picture that Uzumi gave her to Kira and Athrun, and they’re both shocked to learn that Cagalli is Kira’s sister. At the Carpentaria base, Rau, Yzak and Flay board a space shuttle and depart Earth. Flay is scared, but Rau reassures her that he won’t let anything happen to her. At the Victoria base, Shani, Orga and Clotho load their Gundams onto a space shuttle. In the passenger cabin, Azrael recalls how he was beaten up as a child by a Coordinator. He asked his mother why she didn’t make him a Coordinator, and she slapped him across the face and told him that Coordinators are filthy. In the PLANTs, ZAFT soldiers track down Siegel and kill him. Lacus makes a pirate radio broadcast and asks people what the point of the war is. Patrick makes a counter broadcast and accuses Lacus of being a traitor. Kira uses the Freedom Gundam to escort Athrun’s shuttle to ZAFT space. Kira tells Athrun that neither of them can die yet. Athrun returns to Aprilius One, and Lacus asks DaCosta to do something about the situation. Athrun is escorted to Patrick’s office, and Patrick demands to know what happened to the Freedom Gundam and Justice Gundam. Athrun asks Patrick what he thinks of the war and what he hopes to accomplish. Patrick yells at Athrun and asks him if his mind’s been poisoned by Lacus. Athrun asks when the war will end, and Patrick answers that it’ll end when all the Naturals have been annihilated. Patrick pulls a gun on Athrun and again asks him about the Gundams. He summons the guards and tells Athrun that if he doesn’t answer, he’ll be declared a traitor. Athrun charges at Patrick, but Patrick shoots him in the shoulder. He orders the soldiers to interrogate Athrun and use force if necessary. As Athrun is taken out of the building, he attacks the guards and breaks free. DaCosta, disguised as a soldier, helps Athrun and takes him to a shuttle. At the launch bay, Andy preps the battleship Eternal for takeoff and is joined by Lacus. Her supporters remove some of the crew from the ship. The hangar door’s unlock code is changed, but Andy fires the ship’s main cannon and blasts through. On the Vesalius, Rau receives the pursuit order, but since he can’t catch up with the Eternal, he decides to let the Jachin Due forces take care of it. DaCosta and Athrun board the ship just before a large force of GINNs attack. The GINNs fire off their heavy weaponry, but Kira arrives and disables the suits, allowing the ship to escape. The Eternal docks at the abandoned Mendel colony where the Archangel and Kusanagi are hiding. Andy says hello to Murrue, and she says she’s surprised to see him. Kira tells Andy that he has every right to want to kill him, but Andy says he doesn’t hold a grudge.
Cagalli tells Athrun that he has a habit of getting injured, and he tells her that her stone protected him. She asks Athrun if it’s okay for Lacus to be with Kira, and he says that she’s no longer his fiancé. He says that he’s an idiot, and Cagalli says that Kira is an idiot too. Lacus tells Kira about her father’s death and cries in his arms. Outside, the Alliance’s Archangel class battleship Dominion fires its Lohengrins at Mendel. As the Archangel exits Mendel, Natarle calls from the Dominion and tells Murrue it’s unfortunate that they’re meeting under such circumstances. Natarle asks Murrue to surrender and says that she’ll speak on her behalf to the Alliance. Murrue refuses and says that she has problems with the entire Alliance. Azrael laughs at the situation and orders the Gundams to launch. He vows that he’ll destroy the Archangel once and for all. Kira launches in the Freedom Gundam, followed by Mu in the Launcher Strike Gundam, Athrun in the Justice Gundam and Dearka in the Buster Gundam. Shani and Orga attack Kira, and Dearka and Mu destroy several Strike Daggers. Orga fires his chest cannon at Kira, but Athrun goes into SEED mode and blocks the shot. He charges forward and pushes the energy back, damaging the Calamity Gundam in the process. On the other side of Mendel, the Vesalius and two other Nazca class ships watch the situation. Rau decides that he and Yzak will launch and gather more info from inside Mendel. Mu feels Rau’s presence and heads for Mendel, followed by Dearka. Inside Mendel, Rau’s new GuAIZ and Yzak’s Duel Gundam cross paths with Mu and Dearka. As Rau and Mu fight, Yzak attacks the Buster Gundam, believing that someone else is the pilot. The Dominion retreats, and the Archangel returns to Mendel. Kira decides to enter the colony to check on Mu and Dearka. Mu ejects the Launcher equipment and attacks with his knives. Rau uses his extensional arrestors to knock off the Strike Gundam’s right arm and damage the cockpit, injuring Mu. As the Strike Gundam crashes, Rau says that the child can’t defeat the parent. Dearka repels Yzak’s assault and calls out to him. Kira arrives and disables the GuAIZ. Rau exits the cockpit and shoots at Mu. Mu follows Rau into a nearby building, and the two trade fire. Kira enters after them, and Rau says this is his birthplace. Kira wonders what that means, and Mu says they’re lies. Yzak holds Dearka at gunpoint and asks him why everyone is betraying ZAFT. Kira and Mu chase Rau through the building, and he throws over to them pictures of Kira and Cagalli as babies, along with a picture of Mu and his father Al Da Flaga. Rau says that Kira’s real father, Dr. Ulen Hibiki, created an artificial womb that would give birth to the Ultimate Coordinator. Rau says that no matter how much humanity learns, nothing ever changes.
Rau and Mu continue to trade fire, and Rau reveals that he is a clone of Al Da Flaga, who funded Hibiki’s research. Dearka tells Yzak that Kira pilots the Freedom Gundam and previously piloted the Strike Gundam. Rau fires and says he will open the final door and end the world. Kira is nicked by one of Rau’s shots, and he tosses a metal shard at Rau that knocks off his mask. Mu is shocked when he sees Rau’s face, and Rau escapes. Outside, Athrun engages Orga and Clotho while the Dominion attacks the Archangel. Yzak tows Rau’s damaged GuAIZ to the Vesalius, and Kira returns to space to help Athrun. Orga fires at Kira, but Kira deflects his shots with a beam saber. Rau returns to his quarters and quickly pops pills to end his panic attack. He calls Ades and tells him to launch all mobile suits so that the Alliance doesn’t get their hands on the stolen ZAFT Gundams. Rau tells Flay that he needs her help, and he gives her a disk that he says will end the war once the Alliance receives it. As the Vesalius closes to attack range, Flay is placed into an escape pod. Rau sends a message out on an open channel that he’s going to release a hostage before entering the battle. Flay’s pod is ejected into space, and she calls out to the Archangel to help her. Kira faces off against Orga and is distracted by Rau’s revelations. The Dominion picks up Flay’s transmission, and Natarle orders Orga to rescue her. Azrael objects and says it may be a trap, and Flay says she has the key to end the war. While Kira is distracted, Clotho attacks from behind and destroys one of the Freedom Gundam’s wings. Kira chases after the escape pod, and Shani and Clotho behead the Freedom Gundam. Kira attempts to continue, but Athrun stops him and tells him he’s in no condition to fight. Under Lacus’ orders, the Eternal and Kusanagi concentrate all their fire on the Vesalius to break through the ZAFT line. As the Archangel passes by, Athrun and Dearka salute Ades before the Vesalius explodes. Flay is brought to the Dominion‘s bridge, and Azrael takes the disk from her. Natarle greets Flay, and Flay cries in her arms. Azrael examines the disk and is amazed to find the specs to the Freedom Gundam, Justice Gundam and N-Jammer Canceler. On the Archangel, Murrue sits with Mu in the infirmary. He recalls how arrogant his father was, and he wonders why it ended up that Rau was a clone of him. Cagalli comes to Kira’s room and is surprised to see another picture of them as babies. Kira wakes up to Lacus watching over him and thinks she is Flay for a split second. Athrun takes Cagalli out of the room so that Kira can be alone for a while. Kira says that he’s not going to cry anymore, but Lacus tells him that it’s okay to cry, so he cries in her lap.
Azrael meets with a committee to discuss the use of the N-Jammer Canceler. They want to use it to solve Earth’s energy crisis, but Azrael wants to take down ZAFT. He says that nuclear weapons are power and expensive, therefore they should be used. Natarle tells Flay that even on the frontline they may not encounter the Archangel, but Flay says that she has to see Kira and speak to him. She says that Rau’s disk was supposed to end the war, and Natarle says that it will, once the enemy is annihilated.The Alliance fleet gathers and commences an attack on the ZAFT asteroid base Boaz. Kira tells Lacus that he questions whether he should’ve even been born. Lacus tells him that people were born to live in the world. She then tells him that she is very happy to have met him. Large numbers of Moebius mobile armors attack Boaz with nuclear missiles and destroy the base completely. Patrick tells Rau that he’s going to go to Jachin Due and fire GENESIS. On the Eternal, Kira and Athrun launch, followed by Mu and Dearka from the Archangel. Kira and Athrun dock with the METEOR weapons platforms and head for the battlefield. While attempting to destroy the nuke-equipped Moebiuses, Yzak engages Clotho. Shani and Orga destroy the attacking ZAFT forces to protect the Moebiuses. The Moebiuses fire their nuclear missiles at the PLANTs, but Kira and Athrun destroy them with their METEORs. Afterwards, the super weapon GENESIS de-cloaks and fires, destroying a large portion of the Alliance fleet. After the battle, Patrick addresses space and says that the barbaric Naturals are attempting genocide by firing nuclear missiles at the PLANTs. Yzak briefly meets with his mother Ezalia, who tells him that he’s going to be moved to the rear. Azrael argues with Natarle about helping other ships in the fleet, and she says that they’ve suffered heavy damage. Azrael insists that they must attack again before GENESIS can be used on Earth. Before the next sortie, Lacus gives Kira her ring and asks him to return to her side. Cagalli tells Athrun that she’s going to launch in the newly-completed Strike Rouge, and he asks her why she’s going to fight. She says that there are things that she wants to do and has to do, just like everyone else. She tells Athrun that he’s more reckless than she is, and that she won’t let him die. Athrun tells Cagalli he’s glad he met her, and the two kiss.
The Alliance fleet launches another attack against ZAFT’s forces around Jachin Due. Murrue visits Mu in the mobile suit hangar, and he sees from her necklace that she was once involved with a mobile armor pilot. Mu vows that he will return victorious and kisses her. A new nuclear cartridge is loaded in front of GENESIS, and Patrick sets the target for the Alliance’s lunar base on the Ptolemaeus Crater. He tells Rau that since he failed to destroy the Eternal, he must ensure that it doesn’t attack the PLANTs. Rau asks if that includes killing Athrun, and Patrick says to stop the Eternal at any cost. Rau leaves and launches from Jachin Due in the Providence Gundam. GENESIS fires again and destroys the Ptolemaeus Crater base, along with the reinforcement fleet that just launched from there. Azrael orders the Peacemaker squads to launch and destroy the PLANTs with nuclear missiles. Natarle says they should target GENESIS instead, and Azrael draws a gun and rails against Natarle for constantly disobeying him. He says that if they destroy the PLANTs, the war will end, regardless of GENESIS. Natarle asks Azrael if he’s trying to take over the ship, and he says he doesn’t have to because he’s the one giving the orders. The Peacemaker Moebius squads launch and head for the PLANTs. Kira, Athrun, Cagalli, Dearka and Mu head to intercept, and Yzak leads a squad of GuAIZs to stop the nuclear attack. The Archangel approaches the Dominion and loads its weapons to attack, and Azrael orders Natarle to retaliate. The two ships open fire and damage each other. Mu senses Rau’s presence on the battlefield and searches for him, and Rau destroys several Strike Daggers. Kira and Athrun destroy the last of the nuclear missiles and are attacked by Clotho. Shani fires at Cagalli from behind, but Yzak jumps in and saves her. He attacks Shani head-on and is seemingly destroyed, but he ejects the Assault Shroud and stabs the Forbidden Gundam in the torso, killing Shani. Rau deploys his DRAGOONs and attacks Mu. Mu asks Rau if this is what he wanted, and Rau says it’s humanity’s wish. Athrun slices the Calamity Gundam in half with his METEOR’s long beam saber, and Dearka fires his combined guns to destroy the Raider Gundam. Mu tells Rau that his crazy visions will never come true, and Rau says that he is humanity’s punishment. Yzak attacks the bridge of Sutherland’s Doolittle and destroys it. When M1 Astray pilots Juri, Asagi and Mayura are all killed in an instant, Cagalli goes into SEED mode and destroys several Strike Daggers. Murrue tells Kira to resupply and destroy GENESIS while she holds back the Dominion. Azrael orders that the Lohengrin be fired at the Archangel, and Flay tries to warn the Archangel to escape. Azrael slaps Flay and pulls out his gun, and Natarle attacks him and orders the crew to abandon ship. As they struggle, Azrael shoots Natarle several times. He fires the Lohengrin at the Archangel, but Mu blocks the shot. He says he knew he could make the impossible possible, and the Aile Strike Gundam is consumed in an explosion. Natarle tells Azrael that he lost, and he shoots her again. Murrue cries out Mu’s name and fires the Lohengrin, destroying the Dominion.
Rau closes in on the Archangel to attack, and Dearka opens fire on him. Rau deploys his DRAGOONs and heavily damages the Buster Gundam. Kira attacks Rau and is barely able to dodge the DRAGOON attack. Rau damages the METEOR and tells Kira that he’s a nuisance. He tells Kira that he shouldn’t even exist. He says that if people knew about Kira, they would all want to be like him, which is why he can’t be forgiven. Kira counters that there’s more to him than just his power, but Rau says no one will understand that. Rau presses his attack and causes more damage to the METEOR, and he destroys one of its engines with his beam saber. Kira spots Flay’s shuttle and ejects the METEOR just before it explodes. Rau fires his beam rifle at the shuttle, but Kira blocks the shot with his shield. He happily looks at Flay for a second, but a DRAGOON fires from above and destroys the shuttle. As Kira cries over Flay’s death, Flay’s spirit appears. Flay apologizes and says she never understood anything, but Kira can’t hear her. She says that she’s free now, and that he doesn’t have to cry anymore. Athrun and Cagalli arrive at Jachin Due, and he ejects his METEOR and says they have to disable Jachin’s controls to stop GENESIS. Rau attacks the Eternal and Kusanagi with his DRAGOONs, but Kira arrives and attacks Rau, destroying several DRAGOONs. Inside Jachin Due, GENESIS’ next target is set for the Atlantic Federation’s capital, Washington, D.C. Athrun and Cagalli blast their way inside Jachin Due while Kira holds off Rau. Rau says that humanity deserves to be destroyed, and Kira says that’s just his opinion. Yuki asks Patrick to stop because half of Earth’s population will be killed by firing GENESIS, but Patrick pulls out a gun and shoots Yuki. Rau damages the Freedom Gundam and tells Kira that he isn’t wrong, because they live in a world where people hate and hurt each other. Patrick says that they must kill their enemies before their enemies kill them. Patrick sets the firing sequence, and a soldier says that their ships are still in front of GENESIS. Yuki shoots Patrick, and the staff evacuates as Athrun and Cagalli enter the room. Patrick tells Athrun to fire GENESIS and dies. The self destruct sequence activates, and Athrun realizes that when the base explodes, GENESIS will fire. Rau tells Kira that no matter what, he wins, because GENESIS will fire when Jachin Due explodes. Cagalli asks Athrun what he’s going to do, and he says he’s going to self destruct the Justice Gundam inside GENESIS to cause a nuclear explosion. Athrun enters GENESIS and detaches his sub-flight lifter to block Cagalli’s path. Athrun sets the self destruct sequence, and Cagalli tells Athrun that to live is a battle. Rau’s DRAGOONs damage the Freedom Gundam, but Kira rushes in and stabs the Providence Gundam in the torso with his beam saber. Jachin Due explodes, and GENESIS fires and destroys the Providence Gundam before it explodes itself. Kira floats in space outside the ruined Freedom Gundam, and Athrun and Cagalli find him with the Strike Rouge. Kira wonders how they ended up where they are.
With only 10 TV episodes to cover, I thought the pacing of the final Special Edition would be better. I was wrong. The editing is just as rough as the previous installments, with scenes moving from one to another with little in the way of transitions. There are some additions to this installment, along with some changes. A new scene at the beginning gives a little bit of background on Azrael and explains where his hatred of Coordinators began. You’ll also get to see Rau’s face when Kira removes his mask. Watch closely and you’ll see the GuAIZ Experimental Firearms Type from SEED MSV get destroyed by Athrun. One change from the TV series is that Clotho is killed by Dearka instead of Yzak. In the TV series, Clotho went insane and was destroyed after the Dominion, but here he gets caught with his pants down doing nothing and is killed by Dearka immediately after Orga. I liked the TV version where Yzak uses Dearka’s guns to kill Clotho. I don’t know why this was changed, aside maybe from balancing things out to give Dearka a Gundam kill. Another major change is the removal of Mu’s helmet from the field of debris after the Strike Gundam is destroyed. This was very clearly done to allow for Mu’s return in SEED DESTINY. This last piece of the Special Edition ends the same way as the TV series, with no added bonus. Like the other SEED Special Editions, this isn’t designed for new fans and only works well if you’ve already seen the TV series.