Alas, Poor Villain: In spite of all the evil and destruction he's responsible for, you can't help feeling just a very small scrap of pity for Gargoyle in his final moments as he realizes his entire life was built upon a lie. The look on Nemo's face in Gargoyle's dying moments is quiet pity for his onetime friend-turned-mortal enemy.
All for Nothing: The conclusion of Gargoyle's character arc. Everything he's done in the show's backstory and across the course of the series (betraying his King, orchestrating a coup, killing his Queen and countless other people) was all done to achieve his dream of restoring Atlanean supremacy over Earth and humanity. And in the end, not only does Gargoyle fail to achieve this goal, but his actions ironically complete the final destruction of the Atlantean legacy. Then just to rub salt in the wound, Gargoyle also learns in his final moments that he was never actually an Atlantean and was in fact a human – the very lower life-form he so despises — and thus he could never have been part of the Atlantean world.
All Myths Are True: Soddom and Gommorah again (after it was previously established back in the early episodes they had actually been destroyed by the Tower of Babel). Given that Gargoyle is turned into a pillar of salt by the light of the Blue Water, the implication is that something similar killed Lot's wife.
All There in the Manual: According to promotional materials, Jean and Nadia's son is named Jean Jr.
Ambiguous Situation: While it's implied, it's also not explicitly stated whether or not the entire Neo-Atlantis organization is aboard Red Noah when it's destroyed. For better and worse, The Movie uses this ambiguity as its catalyst for Geiger and his faction of surviving Neo-Atlanteans.
Art Evolution: All the main character models are tweaked to account for the 12-year Time Skip during the Distant Epilogue (e.g. Jean and Nadia now being in their mid-20s, the Grandis Gang now being in their late 30s, etc.). The brief look of the unmasked Gargoyle during his death is also a tweaked, older version of the character model from Nemo's holographic Family Portrait.
Asshole Victim: Gargoyle (not to mention the rest of the Neo-Atlanteans who blew up along with Red Noah).
Babies Ever After: The Distant Epilogue reveals Jean and Nadia have a young son (Jean Jr.). Electra is raising her and Nemo's child while Marie is now pregnant with her and Sanson's child. Even a now-adult King has a small litter of cubs.
Back for the Finale: Jean's Uncle returns for the first time since the Pilot and for a brief cameo during the Distant Epilogue.
Bittersweet Ending: Gargoyle’s dead, the Neo-Atlantis organization has been destroyed, and the world’s saved. Jean and Nadia (now free of the burden of carrying the Blue Water) earn their happy ending, marry, and start a family. But countless people are still dead, including Jean’s father and Marie’s parents. Neo and Nemo also sacrifice themselves to save Nadia while the souls of Nadia’s mother and the Atlanteans inside the Blue Waters give up their combined life forces to resurrect Jean. And if Nadia’s 20th Century’s similar enough to ours, then the First World War’s a decade away (if not sooner because of Gargoyle’s actions).
Twice for Nadia, after Neo's sacrifice and when Gargoyle sends Jean plummeting to his death.
Gargoyle after Nadia begins to use the Blue Waters to restore Jean — an act that will use up their power and ruin his dreams of Atlantean restoration.
Bond Villain Stupidity: Gargoyle not even dispatching security forces to besiege and storm the N-Nautilus. What, did he really think they weren't going to fire their weapons inside Red Noah? Justified, though, as he's now entirely fixated on Nemo and punishing his old friend in this hour and place of triumph. Everything else is just immaterial.
Body Horror: Gargoyle's death. He's petrified alive into a pillar of salt. For added Nightmare Fuel, David Jones also adds grunts of pain to Gargoyle's petrification in the English dub.
Break Out the Museum Piece: After the N-Nautilus finally gives out, our heroes transfer their flag, so to speak, to one of the ancient Atlantean craft moored inside Red Noah. This craft is also the same production model as the old Nautilus (as was established back in Episode 30), so we get a chance to see what its hull configuration and bridge looked like before Nemo and his crew converted their Nautilus from a spacecraft into a submarine.
Brick Joke: Nadia being a Lethal Chef back during the Nautilus episodes. In the epilogue, she's finally mastered Grandis' cooking techniques...and Jean and their son still look on her cooking with trepidation.
Call-Back: Nemo's final words to Nadia are once again him telling her to live.
Can't Kill You, Still Need You: Essentially why Gargoyle 'saved' Neo by turning him into a cyborg (rather than letting him die in peace) after Tartessos blew up. The Queen was dead by his coup's hands, Nadia was presumed dead, and Nemo had abdicated and fled Tartessos. In order to use the Blue Water down the road, Gargoyle needed a member of the Royal Family and Neo was the only candidate left.
Cassandra Truth: Nemo revealing to Gargoyle he's actually human, not Atlantean, during the latter's death. Gargoyle refuses to believes it, but resignedly accepts it in his final moments.
Dark Lord on Life Support: More or less. Neo is revealed to be one after Gargoyle used Atlantean cybernetics to revive Nemo's son after the Tower of Babel all but killed him (which technically really makes him a Puppet King on Life Support).
Jean, the boy that loves to fly, falls (he gets better).
Nemo is riddled with bullets by the son and daughter he thought he had killed at Tartessos.
Gargoyle, an Atlantean supremacist, discovers he's actually human (and is likwise killed by the very MacGuffin he spent the entire series trying to obtain).
Despair Event Horizon: After having pulled herself back from it (with Jean's help) in Episode 35, Nadia finally crosses it again after Gargoyle kills Jean. Thankfully, it doesn't last long, as Nemo has a way of bringing Jean back.
The Determinator: Gargoyle gets blasted at point-blank range by the Electron Turrets of the N-Nautilus, he’s fatally wounded…and yet he all but drags himself across the floor (with all the crew training guns on him) to try and stop Nadia’s resurrection of Jean and reclaim the Blue Water one last time.
Didn't See That Coming: Gargoyle never anticipated Neo's consciousness and free will would ever resurface after 13 years of being buried beneath Neo-Atlantean brainwashing.
Distant Epilogue: The series coda is set 12 years after the final battle.
After spending the entire series trying to reject the power and legacy of the Blue Water, Nadia finally embraces it in the show's final hour to save Jean — and by embracing that burden, she frees herself from it forever.
By launching his crusade to restore the Atlantean legacy, Gargoyle's actions ultimately instead destroy it forever.
Dying as Yourself: Neo, having thrown off Gargoyle's brainwashing, dies as Venusis la Arwall rather than as the Emperor.
Enemy Mine: Downplayed example with Nadia and Jean's Aunt in the Distant Epilogue. Given Auntie's dislike and distrust of Nadia in Episode 02, the two women obviously had to have reached some kind of accord when Nadia married Jean. What we do learn is that both women are at least united in giving Jean and Uncle grief over their inventions and keeping them in line.
End-of-Series Awareness: After Neo's death, Gargoyle snidely remarks to Nadia that, "The story is over."
Evil Is Petty: While it's been one of Gargoyle's defining traits and flaws throughout the show, killing Jean out of spite is his worst mistake of the series and results in the destruction of his beloved Blue Waters (and his own death). You can see the moment of hesitation where Nadia calls his bluff, too. Gargoyle knows that if he drops Jean to his death, he’s lost his very last piece of leverage over Nadia and regaining control of the Blue Waters before Red Noah is destroyed. But he’s so enraged that this teenage girl is defying him and threatening to ruin his grand, glorious dreams that Gargoyle just can’t help himself.
The Fellowship Has Ended: By the time of the epilogue, the surviving Nautilus crew and their allies have all gone their separate ways in the aftermath of Gargoyle's defeat (though obviously everybody's still in touch as Marie's narration demonstrates). The Grandis Gang has also formally disbanded with Hanson, Sanson, and Grandis scattered to Europe and the United States.
Grand Finale: For the series, though not if you include The Movie (though that depends on whether you count The Secret of Fuzzy as Fanon Discontinuity or not),.
Half-Human Hybrid: While it's not explicitly stated, Jean and Nadia's son in the epilogue is obviously a Human-Atlantean hybrid thanks to Nadia's genetic heritage.
Happily Married: The epilogue shows a now-older Jean and Nadia living happily together at his Uncle's home.
Heartbroken Badass: Grandis after Nemo's death. The epilogue implies she still hasn't been able to move on even 12 years later.
Heroic Sacrifice: Three of 'em, and all involving Nadia's family. First, Neo sacrifices himself to save Nadia from Gargoyle's mind-control. He's then followed by Nadia's Mother, who sacrifices her soul and the other Atlantean souls in the Blue Waters to resurrect Jean. Finally, Nemo sacrifices himself and the N-Nautilus to allow Nadia and the others to escape Red Noah and to ensure it and its surviving Neo-Atlantean crew don’t survive orbital reentry. Nemo's sacrifice is also justified because Nemo’s been mortally injured and the Blue Water’s protection is gone. If he’s gonna go out, he’s doing so on his own terms.
Heroic Willpower: Neo makes his un-powered robotic body move by sheer force of will to save Nadia.
Hope Spot: With Neo dead, Gargoyle has lost his puppet king and Red Noah is on a course to burn up on atmospheric re-entry. Nadia also now has control over the Blue Waters and Gargoyle has no leverage over her. The heroes are now holding all the cards and victory is finally within their sights. Unfortunately, while Gargoyle no longer has the Blue Waters, he does still have control over Red Noah's other systems and refuses to go down without a fight...
Hoist by His Own Petard: Gargoyle tries to shoot Neo, but his robot body shrugs off the gunfire. Neo then dryly wonders aloud who it was who replaced his Atlantean body of flesh and blood with iron. Gargoyle can only glower in silent rage.
Humanity on Trial: Sorta. Gargoyle’s Kangaroo Court is still against Nemo for betraying the Atlanean legacy and siding with humans. But humanity’s also for all intents on trial with Jean serving as Earth’s de facto advocate alongside Nemo. His failure to shoot the brainwashed Nadia is cited by as clear proof of humanity’s failings by Gargoyle (and conversely its strengths and compassion by Nemo).
I Warned You: Nemo did warn Gargoyle not to go into the light of the Blue Waters if he wanted to live.
Karmic Death: Gargoyle spent the entire series seeking to obtain the power of the Blue Water. That power ends up literally kills him.
Killed Off for Real: Neo, Gargoyle, Nadia's Mother (again), and Nemo (as well as Red Noah and the N-Nautilus if you're counting the spacecraft as characters).
Last of His Kind: The Royal Family of Tartessos (Neo, Nemo, and Nadia) are revealed to be the only biological Atlanteans on Earth in the Present Day. By the end of the finale, Nadia's the last one standing and thus the very last Atlantean.
Match Cut: The toy plane the adult Marie throws into the wind during the final shot transitions into the familiar sepia-hued plane and Closing Credits.
Okay, Jean, so you can't bring yourself to shoot and kill Nadia. We get it. So, then, why didn't just you toss the gun to Electra? At least she was an excellent marksman and was hitting the target (i.e. Gargoyle) until her ammo ran out.
If Nemo has known all along that Gargoyle wasn't actually an Atlantean, then how much of the last 14 years (the coup, the destruction of Tartessos, and all the deaths on Cape Verde and the Garfish attacks) could've been avoided if Nemo had just told Gargoyle? That said, this can be justified in-universe. Given Gargoyle's utter fanaticism and deep-seated bigotry, Nemo must've known that any attempt to tell the truth would be futile. Nothing would've changed Gargoyle's mind and he only finally learned and accepted the truth in his final moments and with irrefutable proof.
Oh, Crap!: Gargoyle after Neo throws off his brainwashing, then again when the Blue Water's energy begins petrifying him alive.
Only Sane Man: Gargoyle thinks he's the only one acting rationally here. It's not played for black comedy and only underscores just how delusional and insane he's become as everything continues falling apart for him.
Please Wake Up: A desperate, anguished Nadia after Jean's death. Realizing he's truly dead fully pushes her into the Despair Event Horizon (until Nemo helps pull her out).
Pyrrhic Victory: It seems like this will be the outcome of Gargoyle's defeat after he kills Jean. While his resurrection nullifies that, the Nautilus crew's victory is still ultimately bitter thanks to Nemo's death.
Rags to Riches: The Epilogue reveals Hanson founds a very successful automobile company after Gargoyle’s defeat. It’s not explicitly stated, but it's not hard to imagine that the success owes itself to technical inspiration Hanson took away from his exposure to the Nautilus and Atlantean technology.
Rasputinian Death: Gargoyle. After getting shot in the face (albeit not fatally) last episode, he now gets blasted at point-blank range by the N-Nautilus Electron Turrets, barely survives, and then gets finished off for good by the Blue Water's energies.
Retired Badass: The Grandis Gang collectively in the Distant Epilogue.
While it had been obvious for the last few episodes (and even as far back as Episode 22's flashbacks), it's definitively confirmed Neo is a Puppet King and Gargoyle's really the one running the show. Furthermore, Neo isn't just brainwashed. He's a cyborg created out of necessity due to injuries he sustained from the Tartessos Tower of Babel's sabotage (as with Nadia MIA and Nemo deposed, Gargoyle still needed a member of the Royal Family to operate the Blue Waters).
As a species, the Atlanteans are effectively extinct in the Present Day. The last biological Atlanteans were the Tartessos Royal Family, which means that Gargoyle (and by extension his followers) aren't Atlantean, but instead humans. None of them realized it because of the genetic engineering the Atlanteans performed on humanity to mold them in their likeness as a servant race.
Sequel Hook: Despite being the series finale, there is one when Red Noah blows. Upon exploding, sixteen light spheres are released and spread around the world. According to Gainax, these were meant to be giant Adams like the one Gargoyle shows to Nadia in Episode 37. This would be the basis of the plot for in a sequel series that eventually turned into Neon Genesis Evangelion when Gainax couldn't recover the rights for Nadia from NHK.
Stupid Evil: Yeah, Gargoyle. Kill the French boy your Princess loves more than anyone else in the world. That'll motivate her to join the 'winning team' for sure...you idiot. Justified again, though, as Gargoyle's enraged this teenage girl's defyig him and his natural vindictiveness just can't help asserting itself at the worst time.
Taking You with Me: Nadia tries to threaten Gargoyle with this when he orders her to restore control of Red Noah, but it's a bluff and Gargoyle knows it.
The Unmasqued World: Despite the Distant Epilogue, the finale does not have a chance to explore the repercussions of Gargoyle breaking the Masquerade and taking the Secret War public. Even the much-maligned The Secret of Fuzzy doesn't really explore this fallout, either.
This Cannot Be!: Gargoyle when Neo regains his consciousness and then later in his dying moments when Nemo tells him he's not actually an Atlantean.
Villainous Breakdown: Gargoyle for most of the finale. It arguably subtly begins during the previous episode after the N-Nautilus boards Red Noah, then really kicks into gear after Neo regains his sentience and everything starts going wrong for Gargoyle. This then leads into...
Villainous BSoD: The culmination of Gargoyle's Villainous Breakdown. The ruination of his dreams and hopes for a restored Atlantean Empire is crushing enough, but the revelation that he was ‘’never’’ actually an Atlantean and was a human – the very lower lifeform he’s so despised — all along completely breaks him in his final moments.
As he's consumed by the Blue Water's energies, Gargoyle's unmasked face is finally seen in full for the first and only time in the Present Day.
The voice inside the Blue Water is revealed to be Nadia's Mother.
Nemo and Electra's final exchange, with Electra placing her hand on navel when Nemo asks her to look after things. The implication, which Grandis realizes instantly, is that Electra is carrying Nemo's child.
"Where Are They Now?" Epilogue: The closing minutes of the finale reveal the ultimate fates of Nadia, Jean, and the rest of our heroes.
Why Don't You Just Shoot Him?: Zigzagged. Gargoyle finally opts for this as the inevitable outcome of his show trial...except then he has the brainwashed Neo and Nadia do it to punish Nemo. By drawing it out and gloating, Gargoyle gives Elektra time to covertly signal the N-Nautilus to fire on their position, which starts knocking over the chain of dominoes that ends Gargoyle for good.
You Are Not Alone: The culmination of Nadia's character arc, as she finally finds her place in the world and with people who love and support her and vice-versa (and all thanks to Jean).
You Are What You Hate: Gargoyle, the Atlantean supremacist who's spent the entire series taking figurative and literal potshots at hummanity, turns out to really be human in his final moments.
Nightmare Fuel, David Jones also adds grunts of pain to Gargoyle's petrification in the English dub.