As ZAFT, the Earth Alliance and the Three Ships Alliance continue their fight, Lacus begs ZAFT to not fire the Genesis weapon and we see moments of the surviving fighters - the members of Orb, Patrick Zala, a drug-withdrawn Clotho, Rau spotting the wreckage of the Strike and a grieving Murrue. Kira, Athrun and Cagalli head of Jachin Due, but Kira breaks away, sensing something and asking Athrun to watch Cagalli. It seems that a fated duel is about to begin...\\
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On the ''Archangel'', as Murrue continues grieving, the rest of the crew are trying to keep the ship afloat. On the ''Dominion''[='s=] lifeboat, Flay suggests that they head for the ''Archangel'' for safety. Rau closes the Providence towards the ''Archangel'', musing at how disappointing Azrael was in the end. Miriallia catches the Providence on radar, snapping Murrue out of her grief. Yzak is shocked - he doesn't recognize that suit at all. Dearka fires the Buster's rifle at the Providence, but it dodges and unleashes its DRAGOON pods. Kira races in with the Freedom + METEOR and begins to duel the Providence as the Buster is ravaged by the DRAGOON.\\
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Flay spots the battle and calls out for Kira, annoying Rau at the fact that she's around again. As Kira battles Rau, the madman destroys the METEOR's cannons and deflects all of Kira's attacks, ranting that someone like Kira shouldn't exist. Yzak flies to Dearka's side to check on him, but encounters Clotho firing the Raider's cannons at him, shooting the Duel's beam rifle out of his hand.\\
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Kira and Rau continue their duel with Rau ranting that if people learned of Kira's existence, they would want to be like him and seek to create him. Kira brushes these rants off even as Rau tears apart his METEOR. As Clotho loses the last of his sanity, Yzak takes the Buster's Anti-Ship Rifle and seemingly misses the Raider as its beam cannon glances off the Duel's shoulder. However, the Mobile Suit ends up exploding, having taken a direct hit, the Duel finally powering down.\\
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Kira attempts to tell Rau that what he is doesn't make up who he is, but Rau brushes it off, telling him that people would never understand such talk. As the Providence keeps wrecking the METEOR, Kira spots the lifeboat holding Flay. Kira ejects the Freedom from the METEOR and rushes to the lifeboat's side as Rau takes aim and fires. Kira is able to stop the blast with his shield, and he and Flay share a moment of dizzy relief as they share a glance through the sensors of the Freedom Gundam and the shuttle window, respectively...\\
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...But the tender moment is forever ruined as a DRAGOON shoots the lifeboat, destroying it and killing everyone aboard in a fiery explosion. As Kira screams Flay's name in despair and Rau flies off, the ''Archangel'' crew, Yzak and Dearka can only stare in disbelief.\\
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As Kira grieves for Flay and hating himself for failing to save her, Flay's spirit approaches him. She apologizes for her actions, stating that she was scared and confused, but now she understands everything. Her spirit embraces Kira, promising her true feelings will protect him for now on. Kira recovers from his moment and, activating SEED Mode, chases after Rau.

At Jachin Due, the ''Eternal'' and ''Kusenagi'' arrive at the Genesis Station and fires their weapons at it. To their shock, it does no damage thanks to the highly-concentrated Phase Shift Armor protecting the installation. Insided the facility itself, Patrick Zala demands to know how three ships, commanded by a civilian and a bunch of Naturals, have gotten this far. As some of his men begin to waver, moved by Lacus Clyne's words, the infuriated elder Zala orders his men to aim the Genesis at the east coast of North America -- a command that shocks many of them, as it sinks in that their leader means to turn the destructive power of their WaveMotionGun on Earth itself.\\
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Athrun and Cagalli arrive at Jachin Due soon after and the two agree to enter the base and destroy the controls there. Despite the worries, the two head on. Moments later, Rau arrives and unleashes his DRAGOON pods on the ''Kusenagi'' and ''Eternal'', musing in disappointment that he did like Lacus' songs, but the real world isn't a cutesy song. Rau's shocked as the enraged Kira arrives, attacking him and wrecking some of the DRAGOON. As Athrun and Cagalli reach Jachin, Athrun begs the soldiers to stop fighting, but they refuse due to OMNI's use of nuclear weapons. Disgusted by the CycleOfRevenge, Athrun can only start fighting his way past them.\\
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As Kira and Rau fight, Rau rants that the path they are heading for is the ultimate path for humanity - extinction for all as they all should. With Genesis ready to fire, Patrick asks why they haven't pulled the trigger. Ray attempts to reason with the chairman, but he responds by drawing his pistol and shooting him. On the ''Archangel'', Yzak and Dearka dock their damaged Mobile Suits as the bridge crew realize they've lost contact with Kira and the other ships. Kira's fight with Rau goes poorly as the man's words start to eat at him as the Freedom loses its right leg and shield. Kira begins to think back to his early days, and how others spoke of him as Rau continues his terrible rants.\\
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In Jachin Due, Athrun and Cagalli fight their way inside as Patrick rants about how Naturals can't be given any quarter, and that ZAFT needs to fire Genesis so that they can claim complete and total victory. To everyone's horror, he begins working the firing console regardless of the fact that ZAFT's own forces are in the line of fire, loudly proclaiming that they should be honored to die for this final victory. But the dying Ray has enough strength left in him to draw his own gun, and as the rest of the staff watch in shock, he shoots Patrick Zala three times in the chest...moments before Cagalli and Athrun arrive, the latter staring blankly in shock as he sees his neglectful-turned-abusive father fatally wounded.\\
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As the rest of the staff panic and make their escape, Cagalli and Athrun make their way to Patrick. Regaining consciousness and spotting his son, the elder Zala urges Athrun to fire Genesis, flashing back to the Bloody Valentine tragedy as he loses himself in his desire for revenge and conquest. These prove to be his dying words, as he chokes on his last breath before bleeding out in the arms of his distraught son.\\
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By this point, the ''Archangel'' rejoins the other ships, where all crews involved wonder about Kira's whereabouts...and, for that matter, why everyone is escaping. Suddenly, a message comes up with a timer -- Jachin Due is set to self-destruct and the ensuing explosion will cause Genesis to fire. As Athrun and Cagalli escape and, elsewhere, members of the ZAFT Supreme Council are captured by other members, Rau gloats that victory is his - Genesis cannot be stopped and the destruction it will bring will reignite the flames of war.\\
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Realizing there's no other choice, Athrun decides to bring the Justice inside Genesis and self-destruct it. As Cagalli chases Athrun, Kira continues his fight with Rau as he reveals that everything that came to this point was his doing. Kira damages the Providence further by destroying its left arm. Cagalli begs Athrun to not go through with his plan as it'll lead to his death. Athrun is unmoved and sends his sublifter to block the Strike Rouge. Kira's fight with Rau continues with the Freedom losing its right arm, leading Kira to draw his beam saber. As Athrun reaches the core and begins the self destruct sequence, Cagalli catches up, tearfully begging him not to die as well, that living is a greater battle to fight.\\
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Kira's fight with Rau reaches its conclusion as the Providence is disarmed and the Freedom is shot in the head and chest vent. Kira is able to get in close and skewers the suit with his beam saber. As Jachin Due self destructs, Genesis fires, consuming the Providence and peeling away the Freedom's armor as the Justice self-destructs and destroys the weapon. As Lacus and the others worry for Kira's safety among the destruction, a radio transmission is made with the ZAFT Provisional Supreme Council seeking to set up truce talks to end the fighting.\\
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Elsewhere, Athrun and Cagalli climb out of the damaged Strike Rouge and tearfully cling to each other. Outside the ''Archangel'', Birdie escapes, making Sai realize it knows about Kira. Athrun and Cagalli catch sight of the bird and chase after it. Outside the wreckage of the Freedom, Kira floats in space, wondering what kind of world exists now. To his surprise, Birdie arrives, the Strike Rouge in tow. Kira, Cagalli and Athrun cry in joy as they are reunited.

!!Tropes Used in this Episode:
* AxCrazy: Clotho, full stop. Rau Le Creusset also lets his MaskOfSanity drop, going on an extended MotiveRant and gloating that nothing can stop the destruction of humanity now.
* BittersweetEnding: The war finally comes to an end and Rau Le Creuset is finally brought down, but far too many people have died for their own good.
* BreakThemByTalking: Rau does a damn good job doing this, hammering Kira with his nihilistic rants even as their Mobile Suits clash.
* CallBack: Once again, Kira finds himself trying (and failing) to save a shuttle of non-combatants from a his enemy.
* CombatBreakdown: The confrontation between the Freedom and Providence takes a heavy toll on both Gundams, to the point that they've both lost weapons and ''limbs'' before the final blow lands.
* DeadPersonConversation: Played with, unlike most other examples in the series. While the scene with Kira and Flay's spirit invokes this trope, it's by WordOfGod merely an illustration of what Flay could have said to Kira had she lived, rather than a genuine conversation. Whether it actually happened in the shows continuity is debatable. Out of universe, it is clearer on rewatch and with this knowledge in mind (say for a moment of translation issues in the dubbed version), that Kira is scripted and animated to hide the fact that he can't actually hear her. However, in universe, it can be claimed Kira's newly awakened PsychicPowers aren't powerful enough to let him hear her, thus keeping the intended reactions consistent while allowing the scene to actually happen in the show.
* DespairEventHorizon: Implied with Athrun, as he resolves to self-destruct the Justice Gundam to stop GENESIS from firing a third time after his father's death. Thankfully, Cagalli is there to snap him out of it.
* DragonTheirFeet: Though his fellow CoDragons were killed in the previous episode, along with Muruta Azrael, Clotho and his Raider Gundam remain a threat, forcing Yzak and Dearka to deal with him.
* DubInducedPlotHole: Related to the above and only a mild example due to the nature of the scene, but in the dubbed version, Kira does acknowledge Flay's words to him, something that does not happen in the original Japanese script. It doesn't massively change the episode's plot, but it does change the context of the scene somewhat, making it seem like Flay's words were what activated Kira's SEED mode this time, rather than him being enraged in general at everything Rau has done, including killing her.
* {{Foreshadowing}}: Kira would notably suddenly feel unease and returns to the Archangel only to find Rau was attacking it, and Rau detects his attack coming (with the notable "Newtype Flash" effect) and dodge, it something that previously would only happen when he fought Mu. Although that's all that SEED would display of it these are the first hints of Kira's enhanced spatial awareness abilities that he would further go onto develop to the same level of Rau and Mu's in the sequel.
* GoOutWithASmile: Le Creusset spends his last few moments with a smirk, likely because he believes that Earth's about to be wiped out by GENESIS.
* GrandFinale: For ''Gundam SEED'', setting in motion the next chapter that is ''Anime/MobileSuitGundamSEEDDestiny''.
* FreakOut: Clotho, as he's suffering from drug withdrawl and he's got no ship left to return to.
* KickTheDog: There was no reason for Le Creusset to open fire on the Dominion's lifeboat other than for the sadistic thrill of breaking Kira's spirit.
* LastBreathBullet: Despite being mortally wounded, Ray has enough life left in him to pull his own gun and shoot Patrick Zala, resulting in a MutualKill.
* LaughingMad: Clotho, when he's not screaming from withdrawl.
* NoKillLikeOverkill: Rau's Providence Gundam isn't just impaled on the Freedom's beam saber, but vaporized by GENESIS for good measure.
* OhCrap: Rau gets one when it becomes clear that Kira hasn't been broken, and that the Freedom Gundam's coming right at him with its beam saber raised for a killing thrust.
* NearVillainVictory: Rau Le Creusset almost gets a PosthumousVillainVictory, as GENESIS was about to fire one last shot at Earth even as he was fatally wounded by Kira. However, thanks to the Justice Gundam self-destructing in its core, the beam fizzles out before it's able to vaporize anything besides the Providence Gundam...and, ironically, Rau with it.
* ShutUpHannibal: Kira's response to Rau's episode MotiveRant, prior to his final charge:
--> '''Kira''': Even so, there's a world I'm fighting to save!
* TakingYouWithMe: Ray manages to fatally shoot Patrick Zala before succumbing to his own wounds.
* VillainousBreakdown: ''Very'' few of the remaining named antagonists face the final act with calm or grace...
** Clotho, gripped by withdrawal from his drug use and with no way of getting a fix now that the Dominion's been destroyed, goes into a shrieking, laughing rampage that only ends when Yzak shoots him down.
** Patrick Zala starts demanding that his subordinates fire GENESIS, shoots one of the officers when they object to the intended genocide, and spends his final minutes raving about why all Naturals have to die, regardless of the cost, before Ray puts an end to his insanity by way of a LastBreathBullet.
** Rau Le Creusset lets his MaskOfSanity drop, going full LargeHam as he treats Kira to an extended MotiveRant about why HumansAreBastards and why he wants to KillAllHumans.
* WhatASenselessWasteOfHumanLife: Athrun seems to have this opinion as he watches his father die -- despite the latter being an AbusiveParent, he was still hoping to reconcile with him, only to watch the elder Zala die while exhorting him to fire GENESIS and wipe out all Naturals.
* WreckedWeapon: Many of the heroic Mobile Suits and battleships get heavily wrecked by the end of the episode.
* WrongGenreSavvy: In the HD Remaster dub, Clotho spends his last moments believing he's the "hero" while LaughingMad. Yzak shuts him up with a fatal shot from Buster's Sniper Rifle.
* YankTheDogsChain: To a heartbreaking degree. Kira has a chance to make up for his past failure by saving a shuttle full of non-combatants, and ''succeeds'' in blocking the shot meant for them...only, as it turns out, Rau had already lined up another shot with his DRAGOON system, catching Kira off-guard.