So you spent the past 20 hours fighting your way past the forces of darkness, plumbing the depths of hell itself and personally handing the Big Bad's strongest minions their own asses, all to rescue the princess and see her home safely. The princess and the hero kiss, the king hands the hero his just reward, and he sets off, no doubt intending to walk off into the sunset. You can practically smell the credits about to roll...
...and then the enemy superweapon levels the castle, killing the princess and demolishing the surrounding town. You and the protagonist sit there, stunned: what the hell just happened?
As it turns out, the princess was Not Quite Saved Enough.
Sometimes, no matter what the heroes do, destiny (i.e. the writer) just has it in for some characters. Save the princess? You come back later and find out she's suffered a Fate Worse than Death. Rescue the village? The Big Bad burns it later. Recover the legendary artifact? Too bad; there's a mole among the good guys and he smashes it right before the heroes have the chance to use it. This is a very specific and special flavor of Diabolus ex Machina that only happens after the protagonists think they've won, a prolonged Hope Spot capped off with a Shoot the Shaggy Dog moment.
Compare Pyrrhic Victory. Can rely on Cutscene Incompetence. If this applies to an entire setting as opposed to a single character, it becomes Happy Ending Override. See also All for Nothing and Yank The Dog's Chain. As this is often a Death Trope, spoilers will ensue.
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Anime & Manga
Nia Teppelin from Tengen Toppa Gurren Lagann dies in the ending as a direct result of destroying the Anti-Spiral, even though Simon had spent the entire second half of the series trying to save her.
In One Piece, Luffy goes to rescue his brother Ace from the World Government. He fights through the world's worst prison only to find he's at the Marine HQ. So he goes there, and manages to, with the aid of a massive army, rescue him just in the nick of time. Only to have them both baited back by some taunts by one of the Marine Admirals, where they get in a hopeless fight and his brother makes a Heroic Sacrifice to save him.
It was really Ace that was baited back. Luffy was trying to convince him to leave, but then his body gave out at the wrong moment, which Akainu took advantage of.
In Dragon Ball Z Vegeta and Nappa, while en route towards Earth, stop at a planet. There, they overthrow a tyrant, freeing a rebel and his beloved... and promptly blow up the planet as the lovers reunite.
In Fullmetal Alchemist, Ed and Alphonse Elric save the town of Reole by bringing down the manipulative Father Cornello. After seeing he didn't have the Philosopher's Stone like they had hoped, they left. Soon after, Lust and Greed kill the real Cornello, and have Envy impersonate him, splitting the city into two parts. Those who believe Cornello lives on, and those who no longer want to be cattle. These sides fight and cause open civil war, all thanks to the Elric brothers (and Envy). Scar sets up a massive transmutation circle from the streets of the city, and waits for things to play out. Then the fantastic military gets involved, which can only end well. Of course, Ed and Al only learn about as they are assigned to investigate, and everyone they know has been hiding this from them. As the last of the civilians secretly evacuate, the majority of the military forces enter the city. Scar activates his master plan, turning everyone caught inside the city into a Philosopher's Stone. And after that, things only get worse.
Hellblazer: John Constantine and a friend have come across a little village that's hoping to use a discontinued pagan festival to revive their economy. Unfortunately said festival causes people to become a twisted version of whatever they're dressed as and go completely Ax-Crazy. John eventually discovers that loud punk music can stop the effects and has safely hidden his friend and some survivors in a nightclub. He goes to get help and then the village is nuked thanks to a possessed ex-fighter pilot who comes out of the trance a second after letting the bomb go. The moral is don't revive things you don't understand and don't be friends with John Constantine unless you can drive a taxi (and even then--!).
Perhaps the prototypal example is the original Night of the Living Dead. In a movie filled with groundbreaking departures from tradition, this trope was perhaps the most significant. After a heroic struggle, Ben is left the only survivor of a night of mayhem and horror in the farmhouse. The next morning he awakes to the sound of a rescue party approaching the house, but as he peers through the boarded-up windows for a glimpse of his potential saviors, they mistake him for just another zombie and perfunctorily shoot him in the head. The movie ends with a sequence of still images of Ben's lifeless, anonymous corpse impaled on a meat hook and dragged to a human bonfire. No one ever knows who he was or what he went through to survive the night . . . of the living dead.
In the second Tales from the Crypt movie, Bordello of Blood, the hero Rafe rushes to save the female protagonist Katherine after she is captured by Lilith and taken to her to be fed on. At first it seems Rafe made it in time to stop Lilith from biting Katherine and focus her attention on him. But after Lilith is destroyed and the heroes cremate her remains, we find out that Lilith did indeed bite her - but on the leg rather then the neck - and had long since turned her. Which Rafe unfortunately finds out too late at the end of the film.
Drag Me to Hell, where Christine's attempts to escape the gypsy's curse prove to be in vain.
In The Ruins, Amy escapes the ruins, but not without having been infected.
Das Boot has a particularly cruel example. Most of the film deals with the sheer terror faced by the men in a German U-Boat during World War II, including several points where they're nearly sunk by Allied depth charges. Somewhere in the last quarter of the film, the titular submarine actually sinks, but the crew manages to devise a plan, repair the damage, get to the surface, and return home. It seems like the film will have a happy ending as the crew survives and makes it back to port, and then the majority of them get killed in an air raid.
Young Sherlock Holmes has Holmes and Watson successfully save Holmes' love interest Elisabeth before Big Bad Rathe sacrifices her in a ritual killing. Then moments later she winds up getting fatally shot taking a bullet for Holmes as he confronts the villain.
This technically happens in Star Trek II: The Wrath of Khan: The Reliant, which Khan had hijacked, is dead in space and unable to do any more harm to Kirk or the Enterprise, and Khan himself lies dying on the bridge, with all of his fellow Augments dead around him. But then he activates the Genesis Device, and the Enterprise just doesn't have enough juice to get out from the device's detonation radius. Khan dies believing that this trope is going to happen to Kirk.
In the third book of the Tennis Shoe Adventure Series, Harry saves Lamachi from being killed by one of Jacob's warriors. however Lamachi was still badly hurt, and dies of infection only hours later.
And while it doesn't quite stick, due to the nature of the series (time travel) the same happens to Gid in a later book.
War for the Oaks: The Queen of the Unseelie Court has Willy Silver kidnapped in order to pressure the Seelie Court into conceding to them. Eddi determines to save him, recruits allies, and mounts a successful rescue attempt...all for nothing, when her ex-boyfriend Stuart comes out of nowhere with a gun.
The novel Nothing Lasts Forever has retired detective Joseph Leland attempting to save his daughter from a terrorist named Anton Gruber. At the end Leland is able to knock Gruber out a window... only for him to grab onto Leland's daughter and send the both of the plummeting to the pavement below.
Between all of Xanatos Speed Chess players in the Dresden Files, this had to happen eventually. If you think about it, though, Harry Dresden himself is this for the monsters he fights.
Harry saves the day from the Denarians, but Nicodemus hits him with a Denarius, and despite Harry's best efforts, he still ends up playing host to a shadow of Lasciel.
After saving The Archive and Marcone from Denarians, Michael gets shot and shredded pretty badly, almost out of nowhere.
After protecting the framed Morgan from the White Council and Eldritch Abominations par excellence, nearly throwing down with the Senior Council, and unmasking the real traitor... Morgan opens his own wounds saving Harry's life, and the Council officially continues to blame him in order to keep wizards from defecting to the Black Council out of fear or greed.
Harry takes on the entire Red Court and wins, only to be shot right before his first date with Murphy.
After fighting his way through a genuine war just to get to the fight, Harry is unable to protect Lily or save Maeve, even though he figured out and stopped their plan. Maeve outmaneuvered him and Mab to get Sarissa made the new Summer Lady, and Molly the new Winter Lady.
Richard Laymon's Body Rides begins with the protagonist saving a woman from a killer...only for the killer to come back shortly afterward and finish murdering her.
Live Action TV
A Real Life Writes the Plot example appeared in Monk: in the fifth season episode "Mr. Monk Gets A New Shrink", Adrian Monk's psychiatrist becomes a murderer's next target and he has to save him. During the sixth season, the actor who played Monk's psychiatrist passed away, and this was written into the story in the seventh season, explaining that Monk's psychiatrist himself passed away.
Locke spends the episode "Further Instructions" saving Eko from a polar bear. Two episodes later, the smoke monster kills Eko.
Throughout Season 3, Desmond repeatedly uses his precognition to save Charlie's life, but since You Can't Fight Fate, Charlie is still going to die, just under different circumstances. Charlie is in a permanent state of Not Quite Saved Enough, with Desmond having to save him from new lethal danger all the time.
Has happened a lot on Doctor Who. Several times, characters will be rescued by the Doctor and his companions, only to killed a bit later on when the writer thinks they've outlived their usefulness to the story and can't think of anything to do with them.
The new series 5 episode Vincent and The Doctor deserves a special mention. Admittedly it was a Foregone Conclusion as even in universe it is explicitly mention several times that Vincent van Gogh committed suicide. But it's still a little heartbreaking when Amy rushes to see if they saved him. They didn't.
Also happens with another character, who is saved by the Doctor from a horrible fate. He also changed established events by having an A God Am I moment. How does she snap him out of this? By killing herself as soon as she's Earth-side. Oh, and the history is still changed (the other survivors remain alive), so that's all her death achieves.
In "The Angels Take Manhattan", Amy and Rory's final episode, they seem to have defeated The Angels, and everything is back to normal. Then Rory spots his own gravestone, as one last Angel lurks behind him...
Supernatural does this a few times when the people Sam and Dean managed to save die shortly after the heroes leave.
The brothers save the people trapped in a police station by demons and even manage to save the people possessed by the demons. They even gain an important ally in a FBI agent who was pursuing them (thinking they were domestic terrorists.) After the brothers leave, the Big Bad shows up and kills everyone.
After leaving a town where the inhabitants have gone Axe Crazy due to a demonic plague, the brothers leave the two survivors they rescued. It turns out one of the survivors was actually demon possessed, and he quickly kills the other.
The episode of Star Trek: Deep Space Nine titled "The Sound of Her Voice" did this, where a Starfleet captain marooned on a planet with a toxic atmosphere, and running out of antidote, sent out a distress call that was picked up by the Defiant. After following the signal to her location in the nick of time, the Defiant crew discovered that the planet's atmosphere caused a temporal distortion in the communications, and they had actually arrived three years too late to save her.
In Season 2 of NCIS, Caitlin Todd survives being shot by a terrorist thanks to a bulletproof vest, but then she unexpectedly gets killed by a sniper.
On NCIS: Los AngelesDom was kidnapped by terrorists who were hiding in LA the whole time. He's finally found and is just within touching distance when he's gunned down.
In Highlander: The Series, Duncan MacLeod rescues his mortal girlfriend Tessa Noel from a renegade Watcher ... only for a random mugger to show up and gun her down on the street outside when she doesn't hand over her engagement ring fast enough.
On Deadliest Catch, Capt. Phil Harris suffered a massive stroke that should've killed him, but doctors were able to relieve pressure on his brain in time. He was recovering wonderfully, even regaining some feeling in his paralyzed side until he had a second fatal "episode". The few Hope Spots of people relaying good news are heartrending, especially since he died several months before the season premiered.
In Moonlight, Beth's DA boyfriend is kidnapped by a vengeful El Salvadorian mob boss. When Mick and Beth track them down, Mick smacks the mobsters around. As Beth is untying the boyfriend's hands in the car trunk, one of the mobsters shoots the guy a bunch of times. Mick tries to save him (having been a combat medic during World War II), but refuses when Beth begs him to turn her boyfriend. She barely shows up the next episode, still mad at Mick. The following episode, she has forgotten all about the boyfriend and is all over Mick.
In the first season of 24, after being saved twice throughout the day, Teri is killed off in the finale.
Older Than Feudalism: Orpheus goes to the Underworld to recover his dead wife Eurydice. Hades agrees to allow Eurydice to return with him to Earth on one condition: he should walk in front of her and not look back until they both had reached the upper world. He set off with Eurydice following and in his anxiety as soon as he reached the upper world he turned to look at her, forgetting that both needed to be in the upper world, and she vanished for the second time.
.hack: Aura, Mia and the entirety of The World R:1. The original four .hack games end with Kite having secured his place in legend as the "Azure Flame" by saving the MMORPG The World and all the AI in it, including Aura, the daughter The World's creator wished he had, from the malevolent digital sentience Morganna and her Eight Phases. Mia, the purple catgirl who turned out to be one of the Eight Phases, can also be restored at the end of the final game by plumbing the depths of a 100-floor bonus dungeon.
Then we flash forward to the .hack//G.U., where Jyotaro Amagi has single-handedly destroyed everything. The World R:1 is no more, its servers having been destroyed in a colossal fire after Amagi went berserk when his R.A. project failed to bring Aura back after she went missing. More frustratingly, the R.A. project required the data from the Eight Phases, and obtaining this data involved vivisecting Mia. That's right: they killed her off in backstory, after you had to go through all that trouble saving her. Sometimes .hack//G.U. feels like a colossal Take That at the entire fanbase.
Dead Rising has various levels of this depending on which ending you get. Ironically, the game's best ending causes this for everyone. All the survivors you've fought so hard to rescue are carted off and disposed of by the military to keep the dirty secret that's caused the Zombie Apocalypse under wraps. By the end, only protagonist Frank West and the former Big Bad's sister (post Heel-Face Turn) are alive, and even then it's not obvious how they escape (or even if they both do; Frank West is the only confirmed survivor). In a specific example, the death toll includes your temporary boss Brad Garrison, who you have to save from the Big Bad (and gets turned into a zombie anyway).
It doesn't say the survivors are killed in Dead Rising. It's even hinted that they were told to keep quiet in return for safe passage.
Otis leaves a note for you after the military show up that says in the confusion, he managed to steal a helicopter and escape.
Brad is a particularly major example, though. After he gets shot, you have to find medical supplies to make sure he doesn't die from the wound. Then you get further on, and he ends up locked in an underground parking lot with an army of zombies.
In the original release of Resident Evil, Richard Aiken will expire from a poisonous snakebite if you take too long to deliver a serum to him. If you do make it in time, it still turns out to be too late and he dies moments after receiving treatment. This is double-subverted in the remake, however; if you get to him in time, he will recover from the snakebite just fine, only to die in a Heroic Sacrifice later on.
In Call of Duty 4, one of the protagonists, a US Marine, rescues a downed helicopter pilot and gets and his squad evacuates the capital. However, the villain sets off a nuke in his own capital, not only killing destroying most of the US expeditionary force, but crashing the helicopter the Marine was on killing both the "rescued" helicopter pilot and the player, who is only able to stagger out of the wrecked chopper's exit ramp before collapsing and expiring.
Rhapsody: A Musical Adventure has the Frog Kingdom: after Micheal helps you retrieve the Earth Stone, the Jerkass King abruptly has him executed for grossly exaggerated 'crimes', just to keep him away from his daughter. Princess Caroline commits suicide shortly thereafter. While Cornet still technically got what she needed from the whole ordeal, the Mood Whiplash alone is staggering.
Super Robot Wars Original Generation, especially the 2.5/Gaiden. According to the OVA that it's based on, once Kyosuke saved Lamia from the Bartolls, all should be well. So they're free to chat leisurely, right? Then Juergen pops by and shot down Lamia, making everyone think she's dead and Kyosuke failed to save her. It then continues for the true save later in the Duminuss arc, though.
Castlevania: Lament of Innocence. Leon Belmont just saved his lover Sara Trantoul from the vampire Walter Bernhard. Just when Leon thought he could just put everything behind, he found out one nasty thing: Sara has been vampirized and is about to suffer Fate Worse than Death. He's forced to use his Whip of Alchemy to put Sara out of misery, incidentally evolving it to the legendary Vampire Killer. Cue Leon's Roaring Rampage of Revenge. Oh, and the Vampire Killer has her soul sealed within it, for extra suckiness.
Obs Cure 2 has Mei's efforts to track down and save her twin sister Jun all come to naught when they're killed literally right before Mei can reach them. This is just the first of a series of Plotline Deaths that render the player's actions practically pointless, as only two characters survive all the way to the Bolivian Army end.
In Jade Empire, you get to save your village from bandits in the prologue with a bit of help from Master Li, but the village gets firebombed and the population massacred anyway while you're out saving Dawn Star.
The Outcasts from Knights of the Old Republic that a Light Side Player Character saves? They get to their Promised Land, only for Malak's orbital bombardment of the planet to bring everything to ruin within the day. They do actually survive the bombing, but they're left to die a slow and horrible death by being picked off by rakghouls, disease, starvation, and toxic waste.
In Avernum 4, Vahnatai assassins magically ambush the king's adviser in his chamber in the party's presence. The unarmed NPC falls extremely easily in the ensuing battle, but with enough power and quick action it is possible to defeat the assassins before he is killed. He then collapses and dies anyway, from a poisoned wound.
Can happen of a sort in Persona4. If you get the bad or neutral endings, in which Nanako dies and stays in a perpetual coma, respectively.
Metal Gear Solid 2: Raiden goes through a bunch of crap trying to save Otacon's stepsister Emma, and has to guide her and protect for a good part of the latter half of the game, capped off during a sniping sequence where both he and Snake take out enemies while she's attempting to cross a platform. Then Vamp suddenly shows up and takes her hostage. Even after taking him out, Emma manages to get fatally wounded in the process. D'oh!
In Fallout 3, a diplomatic player will be pleased to negotiate a mutually advantageous deal between the Tenpenny Tower residents and the ghouls nearby, letting everyone live together in peace and harmony. (As opposed to the other options, aiding one side and killing the other.) Return a few days later, and you'll find that the ghouls changed their mind and killed all the human residents...
Early in Gun, after saving Jenny on a couple of occasions, you find out she's being held captive. Rushing to her aid, you arrive in time to see her throat cut before getting knocked out.
Every single one of the temporal screw-ups in Time Hollow was caused by the villain futilely trying over and over to prevent his mother from dying.
The Elder Scrolls IV: Oblivion has this happen in the beginning of the game. After you've accompanied the Emperor and his bodyguards through the depths of the capital city, you finally make it to a safe room. The Emperor (who's seen his death in his dreams) then gives you the jewel that is the symbol of his office (and keeps the Legions of Hell out of the mortal world) before one of the assassins that's been trying to kill him pops out of a wall and knifes him in the back.
In Homestuck, Doc Scratch tells the Handmaid that she's fated to serve as an agent of destruction for Lord English, but she wants no part of this. Andrew Hussie himself comes charging in to rescue her and to regain control of the narrative. Hussie effortlessly overpowers Scratch, and the Handmaid leaps out a window to make her getaway—and she is almost immediately recaptured by Lord English himself.
This occurs in Worm when the Slaughterhouse Nine attack the city. Most of the Nine are dead or wounded and Siberian's weakness has been found, but Jack Slash is still alive and escapes. A prediction made by a precog claimed that if he escaped, it would cause the world to end in two years.
A rare, humorous version happens in the Rocko's Modern Life episode "Wallaby On Wheels", where the climax involves Rocko putting his jackhammer hobby to good use to save Heffer from falling into the O-Town Bottomless Pit. He ends up plugging the pit with a massive globe of the Earth, saving Heffer and winning the attention of the girl he'd been trying to woo the whole episode. Unfortunately, the globe cracks apart for no apparent reason, sending Heffer plummeting.
In the Titan Maximum season 1 finale Willy stops the time bomb that will end up with the death of everyone living on Mercury with Six Seconds Left, with Gibbs tied up. Unfortunately, while they were arguing with each other, Gibbs escaped and revealed that he prepared a remote detonator, and his plan succeeded.