As an audience, we expect a story to be played out in a certain order: exposition, Rising Action, climax, falling action, and denouement. In many stories, the climax also serves as the Final Battle. The events that occur afterward are normally devoid of action, serving to tie up any loose ends and create a satisfying ending.
But sometimes, writers like to throw in one last confrontation. Perhaps The Dragon assaults the heroes in one last attempt to kill them, or the Big Bad has a final form that took a while to set up. No matter how it occurs, our heroes will have to battle one more time before the day is saved.
A particularly extreme version of Your Princess Is in Another Castle that occurs just when the plot seems ready to be over. To be a Post-Climax Confrontation, the event must follow some criteria:
The major threat of the day MUST be resolved. The Big Bad is defeated (or there's at least no sign that he survived), there's no sign of The Man Behind the Man, no army waiting outside to defeat the heroes. Examples of this trope are rarely the Big Bad (though both of the Alien examples are exceptions) and are typically an independent force.
This conflict must be settled within the same installment of the story. If the event results in a new conflict told within a different installment (or just ends as a Cliff Hanger), it does not count.
This is the crucial part: there must be closure. Plot threads and character arcs are being tied up. In stories that have a traveling party of characters, the party has begun to split off, returning to their homelands. The Post-Climax Confrontation in these kinds of stories generally happen to a select few of those characters, rather than the whole group.
As this is a twist trope, the final confrontation must be sudden and unexpected. The antagonist being confronted in question may or may not have had foreshadowing that he/she would be confronted. It is when the conflict occurs that's surprising: as the plot and character threads are being tied up.
Finally, this is a final confrontation: there are no more conflicts after this threat has been taken care of.
An 80's (or before) anime version of Jack and the Beanstalk greatly expanded the story, having Jack rescue a princess and fight a Maleficent-like evil witch who had taken over the kingdom in the sky. The good guys prevail and the evil witch is vanquished. All seems well, until her giant son Tulip shows up and chases Jack. Jack is forced to climb down the beanstalk with Tulip in pursuit, and chop it down while Tulip's still climbing after him — thus cutting off access to the kingdom in the sky and the princess.
In 20th Century Boys, this is what the majority of the last two volumes (titled 21st Century Boys) is based around.
In the final episode of Mobile Suit Gundam 00 Season 1, Sestuna has just defeated the big bad, Alejendro Corner, and the GN-Xs have been defeated as well. It seems the story is coming to a close when Graham Aker suddenly arrives, and the two battle till both of their mobile suits explode, bringing the Season to an end.
The last episode of S-Cry-ed takes place after the defeat of the Big Bad, as the heroes tie up some minor side conflicts, then they square off to determine once and for all which of them is the toughest fighter.
In PatlaborThe Movie, the main characters succeed in dismantling the Ark (which they are in too) into the ocean before the typhoon hits it, and the crisis seems to be over. However, when they regain conciousness having survived the events, a virus-infected prototype mecha that one of the characters was controlling emerges from the rubble and tries to kill everyone.
In Rurouni Kenshin (manga only), Kenshin explains to Saito that, due to one thing and another, his body is rapidly deteriorating and soon he won't be able to fight anymore. Thus he offers Saito a duel to settle things once and for all, to put to rest the ghost of their bitter past. Saito declines, stating that Kenshin is no longer the man he wanted to defeat. It's as much bittersweet as it's heartwarming.
Subverted at the end of Samurai Champloo. At the end everything else has been wrapped up and the bad guys have been defeated, so Mugen and Jin decide to finally have their long awaited fight to the death that's been promised since the first episode. But the two's weapons have both become worn and dulled and they're both exhausted from the events of the last several episodes, so when they attempt to fight their swords instantly shatter after colliding and the two both collapse from weariness seconds after. They decided they're fine settling things on a draw.
The Doma arc of Yu-Gi-Oh! ends this way: The serpent god of the Orichalcos has been defeated, everyone's had their souls restored, and the heroes are about to make their escape. Right before Yami Yugi can follow the others, the possessed spirit of Dartz shows up and there's one final episode where he has to finally cleanse Dartz's soul and put it to rest before everything's over.
In The Incredibles, the family defeats Syndrome and they are heading home; when they arrive, they find out that Syndrome has abducted their youngest son Jack-Jack, so they must rescue him and defeat Syndrome again.
In The Simpsons Movie, when Springfield has been saved and everything seems to be fine again, Russ Cargill comes out of nowhere with a shotgun and attempts to kill Homer and Bart. Maggie knocks out Russ with a large boulder, luckily.
In Futurama: Bender's Big Score, after the climatic space battle against the scammer aliens (which ended with their ship being destroyed by a doomsday device), their leader Nudar comes back, having survived thanks to a doom-proof platinum vest to make a last attempt to gain the time code. Lars sacrifices himself to kill Nudar.
In the fifth Dragon Ball Z film, Cooler and his henchmen have been defeated, and the worn-out heroes relax and laugh—when Cooler's Dragon, Salza, re-emerges, Not Quite Dead. He tries to finish the weary heroes off but is defeated by Piccolo.
Film - Live Action
Die Hard: Karl manages to survive being strangled (!), and attempts to kill John McClane one last time after Hans Gruber is killed, but is quickly shot before he can do anything.
The botched execution of Jack Sparrow (and his subsequent escape) in Pirates of the Caribbean: The Curse Of The Black Pearl occur after Barbossa is killed.
In Air Force One, after killing lead terrorist Ivan Korshunov, retaking the plane, and fending off Mi Gs on an intercept course towards them, The Mole attempts to kill President Marshall as he's about to evacuate the plane before it crashes.
The final confrontation between Ripley and the Xenomorph in Alien, the Xenomorph Queen in Aliens and the Newborn in Alien: Resurrection definitely qualify. All occur after the protagonists appear to have escaped.
The last scene of Disney's The Three Musketeers (1993). After the heroes defeat Cardinal Richelieu and Rochefort and save the King and Queen, they're confronted by a group of thugs who started pursuing D'Artagnan at the beginning of the movie. It's been so long since the audience saw them that their appearance is a surprise.
The Spy Who Loved Me: For a moment it looks like Triple X is pulling one of these on Bond, but she changed her mind about killing him once the mission is over — she wants to shag him instead.
Tomorrow Never Dies: After Bond kills Carver, Stamper shows up with Wai Lin as his hostage and tries to drown her and finish him off. Bond traps him in the missile firing mechanism and leaves him to die while he saves her.
Army of Darkness: Ash must blow away a random deadite who attacks his workplace.
Ash: Hail to the king, baby.
In Hot Fuzz, after the final, massive shootout against the NWA and the defeat of Devil in Plain Sight Simon Skinner and the Big Bad Police Chief, everything seems like it's all wrapped up and the cops are all finishing up their paperwork, when suddenly the one NWA member they forgot about bursts into the police station and starts shooting.
The penultimate scene in Serenity is a variation in which nothing actually comes of the confrontation. Having been spared by Mal in their earlier confrontation and subsequently ordered his men to provide medical attention for Mal and his crew, The Operative concedes defeat and walks away; he only kills for his cause, which is now lost. Mal tells him that if he ever sees him again, he might kill him. The Operative replies "you won't".
In O Brother, Where Art Thou? the main characters have already secured their fortune and Everett has defeated The Rival when his wife forces them to return to her old house to get a wedding ring, where they run afoul of the Sheriff (and possible Devil) who has been hunting them throughout the film.
In the Kingdom of Heaven director's cut Balien has a final confrontation with his rival after the siege has been resolved.
The Lord of the Rings may be the most well-known example. The One Ring has been cast into the fires of Mordor, our heroes have gone their separate ways, and the hobbits are ready to return to their peaceful Shire... only to find that it has been taken over by Saruman, and they must take back their home from the evil Men that have enslaved their people. It was omitted from the Peter Jackson films, though the omission didn't stop some filmgoers from experiencing Ending Fatigue anyway.
Both the book and movieCoraline have a perfect example, after freeing her parents, the souls of the ghost children, and escaping from the Other Mother's monstrous form and custom dimension, Coraline is attacked by the Other Mother's hand, and has a comparatively easy fight against it.
In Dragon Flight, after the big bad is dead, the dragons are freed, the war is over, our heroes return home.. only to learn that Dragons have been banished from the kingdom. this leads to quite a bit of shouting, and the interruption of a royal wedding.
And again in Dragon Spear, after Darrym is defeated, Velika is rescued and all seems well..... the baby dragon princess is snatched....
Several Discworld books end this way, in particular when the villain deserves to be dealt with specially after his scheme has been foiled, or who is fixated on getting revenge against the protagonist.
In Hogfather, Mr. Teatime survives the dissolution of his plan in the Tooth Fairy's realm and comes to the house where Susan is governess, implicitly threatening the children while aiming to take down Death.
In The Fifth Elephant Wolf survives a tumble over a waterfall and comes back to the embassy after Vimes. Vimes, being Genre Savvy, expects this and is extremely jumpy until it happens.
In Night Watch, after the battle of the Glorious Republic of Treacle Mine Road, Carcer brings his cronies along to confront Vimes one last time.
Live Action Television
Doctor Who in The Angels Take Manhattan. Amy and Rory get sent back 50+ years in the past just as it seems that everything's fine...
Used in the finale of Power Rangers S.P.D.: the villains' plans are in ruins, , the damsel saved, the major threat is destroyed and The Dragon arrested... when Emperor Gruum (who had suffered a Disney Villain Death earlier) crawls out of the rubble to challenge Commander Cruger to one last fight.
A heroic version of this occurs in the ending of the Wicked musical; After Elphaba has faked her death, Glinda, believing that her best friend really has been killed, returns to the Emerald City, kicks out the Wizard of Oz, and has Madam Morrible thrown in prison. Unfortunately, she promised Elphie she wouldn't clear her name afterwards, so Glinda has to take responsibility for Oz alone while Elphie goes into self-imposed exile with Fieyro.
Baten Kaitos has perhaps the most bizarre example. Xelha and Kalas go off into the Moonguile Forest in order for Xelha to "release the ocean inside of her" when suddenly the head of Emperor Geldoblame (thought to have been killed way back at the beginning of the second disk) pops out of the earth in an attempt to kill them. He is quickly defeated, and nothing more is spoken of it.
In Metal Gear Solid it's much of the same, only this time it's a Metal Gear REX and you're only fighting the pilot — twice, the second time during the escape sequence.
In Metal Gear Solid 3: Snake completes his mission, and is now on his way back to America with EVA; suddenly, they are assaulted by Ocelot. Cue a one-on-one close quarters fight aboard the WIG, and finally an old school pistol duel between Snake and Ocelot.
In Metal Gear Solid 4, the final battle with Liquid Ocelot happens after Snake stops him from destroying JD and, in the process, ends up wiping out the entire Patriot Network instead, destroying the true Big Bads of the series. Though of course, that was Ocelot's plan the entire time.
The twist ending at Pokémon Red and Blue is so famous, it's practically a It Was His Sled. After fighting your way through the Elite Four, your character and his exhausted Pokémon are informed that they're the new champions! ...or at least they would have been, if your rival hadn't beaten the Elite Four moments before you did. Cue the toughest battle of the entire game, with no chance to refresh your exhausted team.
In the main games the Big Bad is usually defeated after getting the 7th gym badge. Except in Red and Blue where the Big Bad is the 8th gym leader. You still have the Elite Four and Champion after that though. Averted in Pokémon Black and White. Subverted in Pokémon Platinum.
Science Girls! pulls this one after our heroines have seemingly prevented the invasion, escaped the alien homeworld via wormhole and destroyed the transporter to Earth. Too bad the alien hivemind got through earlier in the game, had time to start setting up and showed up to kidnap one of your party members.
At the end of Wild ARMs 1, Zeikfried and Motherfried have been defeated, the efforts to drain Filgaia's life have been thwarted, and there's a good chance that its decay will even be reversed. The party takes the teleporter back to the earth and Zeikfried suddenly attacks them on the way down, having separated himself from Mother and becoming Zeik Tuvai.
Mario & Luigi: Partners in Time ends with the Shroob leader and her older sister defeated, their invasion thwarted, and their race wiped out. Not really. As the Toadsworths take the Mario brothers to see a KO'd Bowser, the remains of the Elder Princess Shroob (which had been taken from the final battle) are consumed by him. The result is Shrowser, who the brothers must defeat using only counter-attacks.
Suikoden IV has the final duel with Troy. Leads to an Alas, Poor Villain moment afterwards, as it's noted that they had no real reason to sacrifice their life.
Sometimes employed in Metroid games. Specifically, the "real" final boss of Metroid Prime 2 is Emperor Ing. During the Escape Sequence, you get ambushed by Dark Samus one last time, whom you must quickly defeat within the time limit. In Metroid Fusion, you fight an Omega Metroid under nearly identical circumstances. Both fights are short and mainly just to avert What Happened to the Mouse? and showcase Samus regaining her normal power, respectively.
In the Game Gear game Legend of Illusion Starring Mickey Mouse, Mickey defeats the Big Bad, restores everything, plays a Bonus Stage, and returns to his home kingdom... but then King Pete (who wasn't heard from since the game's first level was completed) shows up and a boss battle commences.
In Onimusha 3, Ranmaru sneaks up on Leon and his family after everything seems to be resolved.
In No More Heroes, the "Real Ending" leads to the long-awaited confrontation between Travis and Henry, despite the original conflict of the assassin rankings having been resolved in the previous fight.
In Dragon Quest Monsters: Joker 2, the game itself takes place on an island you crashed on trying to get to a tournament. Once you beat the boss of the island/final boss of the game, you leave and go to the tournament, which is so incredibly easy and postscript-ish that it's mostly done offscreen save for the (still easy) final battle of it.
In Fallout: New Vegas, after defeating Legate Lanius in the final battle in one way or another, the game is pretty much over. However, if the player takes the Mr. House or the Wild Card path they will then have to deal with the General Oliver and the NCR, who will not accept Vegas as an independent city-state. You'll then have to convince them in some way, or just kill them all.
The entire AwakeningExpansion Pack for Dragon Age: Origins: the Archdemon has been defeated, the Blight is quelled, the Darkspawn are slowly retreating back underground... well, the latter not quite. Turns out, there is one loose end to the Fifth Blight, which needs to cleaned up before the Thaw and rebuilding can settle in. Namely, the sentient Darkspawn Architect, who awakened the Archdemon in the first place, as well as his insane creation, the Mother.
In the ending of The Witcher 2: Assassins of Kings, after defeating Saesenthessis/Saskia and resolving the political conflicts of the game, Geralt gets a message from Letho to have a meeting. At this point, Letho explains his role in the story, after which Geralt has two choices: A duel to the death or just letting the man go on his way.
After the events of volume 1 of Legacy Of Heroes, you have to fight a minor vilain, Sunder, who gathers henchmen and storms the city while the most experienced heroes are still recovering from the fight with the Big Bad.
In the PSP remake of Star Ocean, if Cyuss joined the party then after the final boss is defeated and right before he returns home to his timeline he'll challenge Roddick to a private match so the two can personally see which one of them is stronger. It doesn't matter whether you win the fight or not, but it does affect the dialogue between the two of them at the end.
At the end of Kingdom Hearts II after Xemnas is apparently beaten he traps Sora and Riku into a final, 3-part fight with him before they can return home.
The last chapter of Worm has the Villain Protagonist, Taylor, escape the scene of the Big Bad's defeat after she defeated him by mind-controlled every superhero, supervillain, and miscellaneous parahuman in hundreds of Earths to work together, driving herself insane in the process. She's found by Contessa, The Dragon of Cauldron, and they have a short discussion about doing the wrong things for the right reasons before Contessa shoots Taylor in the head (before she can embark on her plans to control all parallel Earths) in a moment of Dying as Yourself.