Arc Rise Fantasia has one happen to Paula and Luna, the We Challenge You! sidequest involved running around all over the world searching for hidden clues, at the end of the search, the whole thing was revealed to be a prank left behind by Zamuel meant for anyone who happens upon his clues.
Dinosaur Forest reveals the adventures of the Space Opera protagonist had been a hallucination from a prison inmate undergoing severe mental health treatments.
Divinity: Original Sin 2 has one of the possible endings turn out to be this. You trek through the whole game, surviving tons of combat and watching Rivellon torn to shreds left and right, confront the Big Bad Lucian who tells you of his plan to save the world which involves turning an untold amount of people into mindless zombies, including yourselves, and you can choose to accept his plan. If you kept one particular character alive, you can even have your mind restored, but you will still have the ending section talking to all of the various characters angrily pointing out that your choices made their efforts to help you pointless. This ending wouldn't be so bad and could be considered a sort of Non-Standard Game Over, except that the game shows that this ending is the happiest ending for the world. All of the other endings where you actually try to strive for a less tyrannical plan result in objectively worse outcomes for the world.
Futurama. The Stable Time Loop has Farnsworth selling Planet Express and getting his crew killed - because Mom tossed in a Nice Hat sombrero. No matter what happens.
Original The Longest Journey was this so much, it hurts: April goes on an epic quest, discovers that she is supposed to become a Physical God to Save Both Worlds, sees all her friends and acquaintances killed or maimed in process, screws up all her previous life... only to discover that she was, after all, only mistaken for The Chosen One and is, in the end, not really needed anywhere. Of course, one could argue that she did save the Twin Worlds but... The sequel Dreamfall: The Longest Journey gives us a rare glimpse of how the protagonist of a shaggy dog story acts after their meaningless quest. April is understandably depressed and cynical. The series then doubles-down on the shaggy dog aspect by having another character be told throughout the entire game to SAVE APRIL RYAN, only to show up just in time to see April stabbed to death.
In Hellgate: London, the humans are trying to kill Sydonai and expel all the demons from Earth. After you kill Sydonai, Murmur appears to tell you that he use you to kill Sydonai so he can get his position, and there's no indication that the demons are leaving just because Sydonai was killed.
When you pick up Elika's body and slowly walk outside while carrying it, the credits start rolling. When you put Elika's body back down outside the temple, the credits stop. The official strategy guide for the game even states outright that this is a good place to stop if you don't want a bad ending. The player still controls the Prince, but there's nothing left to do aside from destroying the tree of life and freeing Ahriman - which the player must do themself, without any coaching from the game. Doing so leads to the downer ending where The Prince frees Ahriman and revives Elika, who responds to this by asking "Why?"
The epilogue expansion turns this around. The prince does not believe that Ahriman can be properly sealed anymore so the choice ultimately came down to fight Ahriman now with Elika and Ormazd's help, or fight him later without them. Elika still thinks he's an idiot for making that choice.
Prince Of Persia 1 allows you to play to the end after you run out of time, to find the Princess's room empty, with her either dead or married to Jaffar.
The main goal of the hero of Diablo is to rescue Prince Albrecht, who was kidnapped into the Tristram cathedral by the insane Archbishop Lazarus, before he can be used as a sacrifice to revive Diablo. By the time the hero gets there, Albrecht has become Diablo's host - the hero is forced to kill him, and then drives the soulstone containing Diablo's essence into their own body in an effort to contain him. While the original game plays this as a heroic act and the only remaining option under the circumstances, the second and third games make it clear that the hero (retroactively identified as Albrecht's older brother Aiden) was being influenced by Diablo all along. Rather than containing the demon, Aiden quickly succumbed to Diablo's corrupting influence and became his new host.
The plot of the Neo Geo shooter Cyber-Lip has the protagonists being sent to a space colony in order to destroy an insane supercomputer who controlled an army of androids supposed to protect humanity from marauding aliens. After destroying the eponymous computer, the ending shows that your Mission Control is actually an alien spy who sent you there to clear the way for an alien invasion.
Both of the first two Monkey Island games deploy this trope comedically.
Chapter one has Guybrush trying to complete The Three Trials so he can get some alone time with Elaine. As he finishes the third trial, he returns and discovers that Elaine has been kidnapped by LeChuck.
The second half of Chapter one has Guybrush buying a ship and assembling a crew to sail to Monkey Island. After he does so, the ship turns out to be in terrible condition and the crew turns out to be extremely lazy.
The third chapter has Guybrush attempting to infiltrate LeChuck's pirate ship and rescuing Elaine, only for LeChuck to leave Monkey Island and return to Melee just before Guybrush gets there.
The final chapter involves Guybrush attempting to rescue Elaine, only for her to escape the villain's clutches on her own, and he bungles her attempt to destroy LeChuck. On top of that, Guybrush spends a lot of time searching the potion which can destroy ghosts: but the potion is actually root beer, which can be found in the vending machine on the very island where the game began!
And if that's not enough, the titular Secret of Monkey Island is never revealed.Two games later, LeChuck admits that not even he knows what it is.
There are only two things that are clear from the ending of Contact: The bad guys weren't really evil, and—despite deceiving both Terry and the player—the Professor isn't either. So... why all the drama?
Every entry in the Geneforge series, except possibly the last. Each game concludes its plotline with the player victorious- and usually on a hopeful note for the world at large, if you play right. But then the next game rolls around, and the world has gotten more crapsack, the bad guys more threatening, the good guys less sympathetic, and your achievements in the previous games are barely mentioned. An air of hopelessness and futility hangs over the proceedings by the end of Geneforge 3, and never goes away.
In Kingdom Hearts: Chain of Memories, Sora's story is all about reclaiming his lost memories, but it turns out all of the memories he "reclaimed" were fake, and he lost a lot of real ones. The game ends with him being put in a sleeping pod to have everything set straight, but when he awakes he will remember absolutely nothing from the game itself. True to form, subsequent games, for the most part, act as though it never happened.
Kingdom Hearts: 358/2 Days has a similar plot thread: not only does Xion die in the end, but everyone also forgets she existed in the first place. Subsequent games even cut her out of flashbacks she should appear in. To add insult to injury, her death is meant to help Roxas free Kingdom Hearts and defeat Xemnas, but that plan gets shut down immediately. Then Roxas is absorbed by Sora, who continues to unwittingly serve Xemnas in exactly the same way Roxas and Xion had.
In the ending of The Legendary Axe II, you finally claim the throne from your ne'er-do-well brother, but shortly afterwards a naked assassin chick with purple hair and a scimitar the size of Shaq jumps out of literally NOWHERE and... it cuts to the credits! WHAT.
At the end of Ultimate Spider-Man, you as Peter Parker/Spider-Man have to fight Eddie Brock/Venom to the finish to keep him from killing Bolivar Trask, the man who apparently had something to do with both of your parents' deaths and get your hands on the file which tells you the truth about the incident. During the cutscenes after beating Venom you don't actually get to find out what was in the file and Eddie tracks down and murders Trask in prison anyway.
It's only a Shaggy Dog Story for Eddie, not Peter and the player as we do get to see what was in the file during the final cutscenes. Eddie's father took a sample of his and Richard Parker's (Peter's dad) research, then tried it on the plane, which transformed him into a Venom-like creature and caused the plane to crash. Also, Eddie cites his captivity by Trask and Trask only getting three years as his reasons for killing Trask.
In the brilliantly-written Time Hollow, the intrepid hero finds himself in a completely altered reality, with no memories whatsoever of how it happened and no idea how to set things right. All he has is a mystical pen with the ability to alter something that happened in the past, each time changing his present reality in drastic and unpredictable ways. Sometimes solving a problem creates an entirely different problem, which he must then seek out and fix. After countless twists, turns, harrowing confrontations, and narrow escapes, the pieces ever-so-gradually fall into place (with several pieces falling out in the meantime). It turns out that if the hero goes to a certain location to save a certain person's life, this will avert the long chain of events which caused time to go out of whack, and everything will return to normal. Of course, by then it should be readily apparent that had he just known that beforehand, he could've just done that right away and saved several weeks of trouble. Even better, once you finish the game, you can start a new one and do just that! Meet your enemy on the street, let him know that you're onto his scheme, and offer to set things right. He'll grudgingly give you one night to make good on your offer, which is more than enough. Go to the school, get the pen from your dad, save the girl, done. You even get a special ending for your trouble.
Team Dark's story in Sonic Heroes ends this way for Rouge; she only teams up with Shadow and Omega because she believes that Dr. Eggman has a secret treasure that she's intent on finding. When the Egg Emperor is defeated, she finds that the treasure is a surplus of robotic clones of Shadow, whose status as the original Shadow that fell to Earth at the end of Sonic Adventure 2 was previously brought into question (though later confirmed to be the case in the canon ending of his own game).
Sonic the Hedgehog (2006). A lot of levels have absolutely no story relevance, with the biggest offender being Sonic's campaign, 90% of which is spent saving Elise, only for her to get captured by Eggman again in the next scene. Furthermore, the whole story feels like one for the player since in the end Elise pulls out a Cosmic Retcon.
Although actually, most of the characters, including the player, survive, allowing for the sequel Mask of the Betrayer. However, one of the endings of that is also a Shaggy Dog Story, as you send the curse back into the world, after you were given it in the first place for the sole purpose of getting rid of it. Fortunately, the other three endings do have varying degrees of meaning to them.
A better example is your trial for the Ember massacre. Whether you're found innocent or guilty, the losing side appeals to trial by combat. The developers themselves have admitted you shouldn't have to fight Lorne if you were found innocent.
Then there's the Third Crusade, depending on how invested you are in bringing down the Wall of the Faithless. Two of your companions are bound for it, and another was kicked out of one of the Realms' "heavens" for trying to go against it. Agree with Kaelyn, gather Akachi's old generals, storm the City of Judgment... and then Kelemvor shows up and goes "Nope."
Every ending of Covenant of the Plume is some variant of this. For summary purposes, the hero Wylfred has made a deal with the dark goddess Hel that will help him slay the other goddess Lenneth, who he blames for the death of his father. He's still just an ordinary guy—in no ending can he actually kill her. The degree to which the trope applies varies, however: ending B is straight-up shaggy dog, with absolutely nothing achieved. In ending A, Wylfred decides on his own to give up on vengeance, and kills a powerful servant of Hel. Hel herself remains untouchable, despite the revelation that she was responsible for all the suffering and death that occurred after the first fifth of the game. C fits into another trope...
In Final Fantasy X, if the story had ended as planned with Yuna sacrificing Tidus as the Final Summoning, and having him become the next Sin, this is exactly what this would be. Thankfully, the game averts this. As it is, it needs Final Fantasy X-2 to avert a Downer Ending.
In the A Crystalline Prophecy add-on scenario for Final Fantasy XI was a cross between a Shaggy Dog Story and All Just a Dream. You can get some actual decent gear rewards from the missions, but the story itself would have resolved in the same manner had you not been involved, not to mention that none of the NPCs involved remember anything that happened or mention it ever again.
The Final Fantasy XIII-2 is REALLY CRUEL about this: due to your actions, Chaos Reigns, Caius has goaded the hero into killing the goddess Etro, and most of the human populace that you've spent making a better life for is culled so that only the most hate filled and traumatized humans thrive on a small patch of land so that they can torment the drifting souls within Chaos with their angst, creating monsters of suffering. That's right, the happy ending you won in the first act is only reserved to the bitter end for the most screwed up people that Coccoon could spit out.
In Final Fantasy: The 4 Heroes of Light, Aire is turned into a cat by some cursed treasure. When a black cat turns up at Jusqua's door, he realizes what happened and blames himself for ditching her for her Royal Brat ways. He proceeds to take the cat on a long trek to Urbeth, where he must raise 10,000 gold for a sorcerer to remove the curse, running around on various errands for the merchant lords and working a shop counter—then the sorcerer steals the cat when he flees the city, and Jusqua has to cross the ocean to the Grim Up North in pursuit (where he joins up with Brandt again). Then the cat escapes from the sorcerer. When Jusqua panics, Brandt is quite baffled and then blithely remarks about the time he'd spent traveling as an animal with Aire the white cat, in a completely different part of the world, before they found a way to turn back on their own. Jusqua's response to this revelation?
In The Lost Crown, you can have Nigel collect photos and recordings of various hauntings, as well as find the legendary Saxon crown. In the end, he not only has to return the crown, but all his hard-sought ghost evidence is sabotaged.
At the end of Nelson Tethers: Puzzle Agentthe foreman you were trying to save is taken away screaming by the Hidden Ones. Tether's superior doesn't care about this in the least since the eraser factory is open again... despite the fact that the President (the factory was the main eraser supplier for the White House) didn't even notice the eraser shortage.
This is averted in the sequel where you go back and finally solve the mystery of the Hidden People and the astronaut
Episode 3 of Strong Bad's Cool Game for Attractive People starts with Strong Bad's game console breaking. He then sets out to form a "Battle of the Bands" to raise the repair money. After getting all the local bands, having to enter himself with two characters he hates, and barely managing to etch out a win, he spends all his prize money on the machine, only to find there was a piece of cheese wedged inside, and all he had to do was pull it out.
Episode 1 also qualifies: while Strong Bad literally achieves his goal of beating the snot out of Homestar, his briefly successful efforts to ruin Homestar's life - specifically, turning him into a publicly disgraced criminal fugitive without a girlfriend - are undone by Strong Bad himself when he has to kick Homestar out of his house.
At the end of the second episode of Hector: Badge of Carnage you find out that you had all the needed evidence from the beginning and all you needed to do was to wait a few hours for the forensic examination to finish. This annoys Hector since it means that he did not have to drug a restaurant full of people and burn down a church
Touhou Project has this in several storylines. Several times, the incidents Reimu and Marisa set out to stop are just some people they don't know temporarily doing something fairly harmless for personal reasons, and didn't bother to tell others, and the plot would have been resolved if nobody had ever tried to resolve the incident. Of course, since there's a climactic (if pointless) battle, and Defeat Means Friendship, the only real result of the story is "Reimu meets new friends".
Immaterial and Missing Power features a plot based around finding out who was causing mysterious parties to take place. When they find out it was just a Hard-Drinking Party Girl oni looking for an excuse to get drunk, they just go ahead and have the parties anyway.
Imperishable Night involves exiled lunarians trying to hide the Earth in a bucket, but failing at making it work properly, so they were going to just abort the plan, anyway.
Phantasmagoria of Flower View revolves around a very large cast of playable characters, many of whom don't even care about the event or want to stop it, anyway, finding out that the incident is a natural occurrence and harmless to begin with.
Mountain of Faith's plot is a new shrine appearing on top of the youkai mountain and telling the Hakurei Shrine that they'd be absorbed. Not a major incident, but certainly cause for some concern. Except that when you get to the god of the shrine they turn out to be perfectly reasonable and the whole 'you will be assimilated' thing was her miko being over-eager.
Undefined Fantastic Object has youkai subordinates of a sealed priestess rescuing her... but she turns out to actually be fairly nice, and was sealed for wanting humans and youkai to get along. Since the modern era is one of peace to begin with and the totality of her plan is establishing a temple, the characters don't really mind letting her go free.
Ten Desires sees hordes of divine spirits appearing. It turns out that this is a side effect of someone powerful reviving... and she finishes doing so before the PC gets there.
Silent Sinner in Blue is probably the most egregious example, as the entire thing is a giant Gambit Pileup where one of the plotters decides at the last moment that she'd rather just get drunk than actually achieve her objective, and steals the lunarian's booze instead of their legendary treasures.
Silent Sinner in Blue is a Shaggy Dog Story. The overall story, Bougetsushou, is not. The full ending is in Cage in Lunatic Runagate, where it turns out that this was all a plot to put the fear of youkai (mostly Yukari, really) into Eirin, and the sake was a perfect choice for doing that.
The first Doom. You fight through hordes of monsters, including literally going to Hell and back... only to find on your return to Earth that the demons have already invaded. And their first victim was Daisy, your pet rabbit.
Played for laughs in Rex Nebular And The Cosmic Gender Bender. The titular protagonist is sent to a Gendercide-ridden planet to retrieve a valuable vase. Over the course of the game, he loses his ship, destroys a large city, causes the deaths of several people, kills a small dog, suffers through repeated bouts of gender-bending, and gets kicked in the nuts, not to mention averting several deaths by a hair along the way. In the end, he accidentally breaks the vase in front of his customer while arguing about payment. Which they had already agreed on, note.
By Word of God (there would have been a sequel-TC, but it seems to be Vaporware), the Voinian story in Escape Velocity Override is this: all storylines happened, but where all the others had a big impact in some way, the Voinian storyline is effectively rendered moot by the UE storyline — you kill one of the UE's Admirals, but Vice Admiral D'Erlon is talented enough to pick up the slack, you bomb the Emalgha's mining planet into dust, but they still maintain enough production capacity to help the UE offensive, you devastate one of the UE's colonies, but it isn't important enough to cripple the UE... all culminating in the Voinian officer you report to making references to a superweapon project sure to bring the UE to its knees, but it is too important to let humans in on the project — Word of God is said project is the Voinian Dreadnaught, which you destroy in the course of the UE story before it even reaches UE space.
Mario & Luigi: Superstar Saga: The second half of the game reveals Peach's voice was never stolen to begin with — it was Birdo's voice that got stolen. Peasley heard of Cackeletta's plan beforehand and warned her, but she beat Mario to it before Peach could tell the truth.
Saving galactic civilization is rendered moot when the relays explode- without them, galactic society can't function as practical FTL is now gone. The Victory Fleet can't even get back to their home sectors.
All of your True Companions? Well, they're stranded on an unknown planet now with no way out due to the Normandy crash landing there.
The Citadel explodes, presumably killing every single lovable character there in all the sidequests you did.
The most visible case involves the Geth War. The most popular ending, Destroy, kills all geth and any other AI in the galaxy as a sacrifice to take out the Reapers.
Via Inferred Holocaust, saving Earth becomes this, since not only will the destruction of the relays ensure a new dark age, but the entire Citadel blowing up above the planet will result in very bad things for the people below.
The Expanded Cut DLC retconned a lot of the endings, removing, among other things, the Normandy crashing (well, it still does, but it gets repaired quickly and the crew leave to reconnect with the rest of the fleet), the relays exploding (now, they simply break apart and are easily repaired, letting galactic civilization go on), and the Citadel blowing up (it doesn't blow up in the Synthesis and Destroy endings, as opposed to the original endings, where it did). However, it added a new ending that is a true Shaggy Dog Story: The Reapers win, meaning that essentially all the crap Shepard goes through was for nothing. At least in this cycle.
Amusingly enough, one of the original endings still exist in the Extended Cut... as the Destroy ending you get when your preparations have been poor. The accompanying narration is also fittingly bleak.
In Kid Kool, the goal is to save the king, who is dying, by finding the "seven wonder herbs." If the player doesn't finish the game quickly enough, the king dies before you even get to the end.
In the Game Boy game Final Fantasy Legend I, the heroes live in a world that's a giant tower climbing to heaven. They decide one day they want to see what's at the very top. They spend the entire game climbing the tower, and eventually defeat the Creator at the gate to Heaven. Then they decide to just go back home.
While Mondo Medicals was a Shoot the Shaggy Dog story, the sequel, Mondo Agency, settles for just a plain old Shaggy Dog Story instead, with the player going on a mission to stop an assassination attempt on the president and ending up accidentally killing him themself and getting fired.
In the Modern Warfare mission "Heat", you fall back from the enemy's counteroffensive to a planned landing zone at a farm, only to find out that it's too heavily guarded by SAM sites, then you have to trek back down the hill you just surrendered to the enemy to reach the new LZ.
Kitana's ending in the sequel both alleviates and worsens the dog killing. Turns out she survived, united the realms and defeated Shao Kahn returning to be Queen of her realm. But it is now only a vision and the timeline is in many ways worse then the original.
In Fallout, the whole Great War, brought by a lack of resources, turned out to be this. A few weeks before the nuclear bombs fell the Big Mountain research institute had developed matter replicators that would have made lack of resources a non-issue.
Fallout 4 does this to Elder Lyons' offshoot of the Brotherhood of Steel from Fallout 3. Lyons left the BOS in the west coast, who were notorious for hoarding pre-war technology and taking it from others (sometimes by force) and started a new BOS dedicated to protecting the Capital Wasteland from Super Mutants and using collected technology for the betterment of the people. While they made a lot of headway in protecting the peace, by the events of Fallout 4, they not only revert to their tech-hoarding insular ways, but evolve into a fascist military organization that rules over the east coast like feudal lords.
The Jamaica Plains treasure seems like it's lifted straight out of Cowboy Bebop. Said treasure is actually something quite valuable and worthwhile: baseball history, Indy car champions, lots of red white and blue, scenery, a celebration of America. In game however it's worthless apart from your companion's reactions.
Fallout: New Vegas allows the player to invoke this on either the NCR or the Legion. Or both. In the 4 years since the Battle of Hoover Dam, both sides have been suffering losses, trading victories and defeats, trying desperately to gain ground. Then, out of the blue, a simple Unstoppable Mailman can ruin both parties claims to Hoover Dam by either siding with Mr House or choosing an Independent route, forcing both sides to retreat.
BioForge: Not at the end, but late in the game, once the hero finally learns his past identity, he concludes that it doesn't matter, as - by this point - he can never be that person again.
In retrospect, Might and Magic VIII moves towards this. You save the world... which is then destroyed for unrelated reasons a couple of years later (likely as little as one or two).
The plot of Dragon Age II might qualify, as Hawke never instigates any events, only reacts to them. Even saving the city from the qunari doesn't really count, as the rest of the Free Marches would have stepped in soon. Regardless of whether Hawke sides with the mages or templars—and that comes down to only one decision—you can be as pro-mage as you want in the first three acts and still join the templars, the ending is still the same: Hawke on the run, Meredith and Orsino dead, war between mages and the Chantry.
On a related note, this is also the Arishok's journey in a nutshell: He is stuck for years in Kirkwall because he is searching for the Tome of Koslun, which was stolen from the Qunari. If you managed to keep appease him by returning it along with its thief (under special circumstances), he will loose both again and return to his homeland to be punished, demoted and replaced by Sten from Dragon Age: Origins. If you choose to fight him, he will end up dying but not before vowing his people will return. Turns out that the Qunari denounced his unsanctioned attack on Kirkwall to not risk another Exalted March with the Chantry, retried the survivors and agreed to never speak of this again, making the Arishok's dying threats hollow. Either way, his journey will end in failure.
In Star Wars: The Old Republic, the Imperial storyline on Taris (a planet which was basically wiped out by orbital bombardment in Knights of the Old Republic) apparently happens sometime after the Republic storyline- but in the same place. Which means that after your Republic character single-handedly saves the Taris restoration project, you go back with a Sith character and learn that everything you did has been completely undone. Notably, Republic characters have the option of sending a Jedi to teach a group of Force-sensitive rakghouls how to use their abilities, nicely subverting the rakghouls Always Chaotic Evil characterization in the process. Imperial characters can go to this same group, defeat the Jedi, and convince the rakghouls to go straight back to evil.
The same happens in reverse, but on Balmorra. While Republic players are busy saving the recolonization effort(s) on Taris, Imperial players are taking over Balmorra and securing its weapon production for the empire. However, someone might go on with a Republic player and watch as everything the Imperials did to secure Balmorra is essentially undone, as the Imperials are run off the planet.
Speaking of Taris, it's the first level of Knights of the Old Republic following the introductory tutorial. The player spends anywhere from three to six hours at least running around doing various quests on the planet, only for the previously mentioned orbital bombardment to make all of it meaningless, as all the characters you just helped are now dead.
Particularly heartbreaking when it's revealed in Star Wars: The Old Republic that the group of refugees you guided towards "Sanctuary" in Knight of the Old Republic all died on their way there.
Howeever, the aforementioned elf princess knows of a potion from her village that (in her own words) might get rid of the cat ears. The might still keeps this open as a Shaggy Dog Story, as we never do figure out whether it works or not.
There is a questline in the Dread Wastes where a group of pandaren brewers are attempting to use mantid ambernote which has healing and lifegiving properties in this universe to brew a new variety of beer. The questline is long and complicated and involves gathering two special blades, enchanting them with a specific spell that only sprites can use, and venturing into the heart of mantid territory to do all of this. In the process, you even free one of the Klaxxi Paragons. And after you go through all this trouble, what's the reaction to this radical new variety of beer?
Sapmaster Vu: Yeah, this is pretty horrible.
Slightly subverted at the end, where it's discovered that the nasty beer can be used to revive Pandaren that had been frozen in amber and presumed dead.
The Horde war campaign in Battle for Azeroth ends this way. The player hunts down a long-lost shipwreck to revive its captain and the lost Prince of Kul Tiras as Forsaken, recruiting another dying human along the way. The captain is senselessly killed without ever saying a word on-screen but the player succeeds in stealing a powerful Kul Tiran artifact. In the follow-up to the campaign, the Alliance steal the artifact back and it ends up being destroyed while the recruited human is executed by Sylvanas and the Prince escapes from Horde custody, rendering all of the player's efforts pointless.
Both factions in Battle for Azeroth recruit their new allies to secure fleets capable of waging war on their enemy. The Zandalari fleet is destroyed by sabotage while the Kul Tiran fleet is destroyed by Azshara, without either fleet having actually fought anyone.
While Red Dead Redemption ends with Shoot the Shaggy Dog, Seth's missions end with this trope. You go through a lot of trouble to uncover the treasure he demands you help him find before he helps you attack the fort. The treasures turns out to be...
Seth:A glass eye?!? IT'S A GLASS EYE!
The whole revolution in Mexico, as would be expected when it's spearheaded by a playboy megalomaniac. Reyes got what he wanted...
The entire story (and everyone who died in it) was a local politician attempting to erase his gang past and get military credit before the big election, by ordering assassinations on his former brothers-in-arms including John. Then he gets impeached.
In Shadowrun Returns, your main objective is to receive an inheritance from your old pal Sam by solving his murder. After a convoluted plot involving a serial killer, a religious cult, a hive of demonic insects, and the family dramas of some rich elves, you catch the culprit only to discover that Sam was straight-up lying to you. He had no inheritance to leave, and just wanted to see if you cared enough about him to bother. But at least you saved Seattle from being overrun by the insect queen and if you played your cards right, you got said rich elves to give you a lot of money and/or a cushy job.
While Portal ended with Chell killing GLaDoS (kind of) and escaping the Aperture Science compound, a later update added a Sequel Hook where she's simply captured afterwards and dragged back inside for more experiments.
Portal 2 ends with Chell finally being freed for good, but in a world that's at best uninhabited and at worst under the control of a genocidal alien regime. GLaDOS learned to feel compassion over the course of the game by realizing she's part human, but in the end she deletes that part of herself, leaving her more sociopathic than ever. The multiplayer campaign is about gaining access to a vault full of living humans in stasis (up to this point humanity was presumed extinct), but after finally doing so, GLaDOS kills them all within a week via her cruel "experiments." And Wheatley, who became drunk on power after all the trouble he and Chell went through, is stuck in outer space with no way home.
The entire plot of Life Is Strange becomes one if you choose the "Save Arcadia Bay" ending; in order to prevent a tornado from destroying her hometown, Max will be forced to travel back in time and allow her best friend Chloe to be killed, despite having previously used time travel to save her and spending the whole game afterwards trying to help her out. To make matters worse, the mystery they were both attempting to unravel (the disappearance of Chloe's friend Rachel) will end up being solved regardless when Chloe's killer gets arrested and rats out the person responsible, meaning that from a narrative perspective, there was never a good reason for Max to save Chloe in the first place.
The heist Trevor arranges in Grand Theft Auto Online ends up being this for him. After getting all the product he needs for a huge drug deal (and paying off the heist crew that helped him out), it turns out the deal is a sting operation by the DOA, and Trevor is forced on the run.
In Pillars of Eternity, several of the companions' personal quests end in disappointment and a lack of resolution:
Edér never does find out why his brother joined Waidwen's army.
The tablet Kana's been looking for was destroyed a LONG time ago, and the scholar is undead and is hardly the role-model that Kana thought him to be.
The reincarnated elder Sagani spent five years looking for is a stag, and she gets there just in time for him to die.
Zahua's vision quest reveals nothing except what he already knew all along: that the Tacan people and its culture are gone and there's nothing he can do about it. The vision is simply telling him that he needs to let go of the past.
A bunch of subplots in Batman: Arkham Asylum can be consideded this. Batman goes through a lot of trouble to save people from the escaped inmates only to return later and find out that they were killed off-screen when he was away. At some point he has to track down a doctor and once he finds her he has to carefully make sure homicidal maniac Victor Zsasz doesn't kill her, only for her to be killed by a trap less than a minute later.
The entire plot of Batman: Arkham City is this from the Joker's point of view. He goes through all the trouble of getting Batman captured, infected with his poisonous blood and even sending packets of his blood to the city to infect random citizens in order to make Batman comply with finding a cure. Later, at the end of the game, when Batman has the cure in hand and is debating whether or not he should hand it over, he has no better idea than jump at him from behind and stab him in the leg, which causes him to drop the vial with the cure, which breaks. As he lays dying, Batman's last words to him are him revealing that in spite of everything he's done, he still would've given the cure to Joker.
Batman: Arkham Knight does this with the Joker-Infected storyline. Throughout the game, we're told that Henry Adams, being the only one of the Infected not to show symptoms, is the only hope for a cure. As it happens, he's just really good at hiding the symptoms - he's just as bad as the others, if not worse. He kills the other Infected and then, on realizing Batman is even more affected than he is, kills himself. The Joker hallucination sums up it:
"Wait a second... if Henry had Mad Clown Disease, then that means there is no cure! You had featherhead slaving away for nothing when he could have been saving Babs!"
Fate/EXTRA's main storyline ends this way: Your desperate struggle to survive ends with you getting deleted by the Moon Cell because you're a rogue NPC. Your Servant expires because their purpose in the Holy Grail War is fulfilled. The Big Bads would have ultimately been stopped and killed by the True Final Boss anyway, making your battles with them pointless. You do defeat the True Final Boss, but you had no idea he even existed. Your human counterpart on Earth cannot be revived due to a medical condition that cannot be treated, and won't be you even if they are. The only gain is one girl you saved at the start of Week 4, and one wish that may still be subject to typical Holy Grail shenanigans.
Another Fate example comes from Fate/Grand Order: Caster of Nightless City's/Scheherazade's goal is to remove herself from the throne of heroes and not be summonable again, due to having an extreme case of thanatophobia. However, she's not story-lockednote although her name is hidden until you reach a certain point in the Agartha singularity, meaning it's entirely possible that by the time you do face her, you've already summoned her.
Darkest Dungeon: The ending in a nutshell: You defeated the eldritch god! Yay! Oh wait, you defeated one eldritch baby. The cocoon at the center of the earth is still alive, still pumping out eldritch essence, and destroying it would cause the destruction of the world. And it has a set incubation date so The World Is Always Doomed anyway. And you're too insane to do anything about it or protect your hamlet from ruin anymore, so you commit suicide. Just to hammer this home, a new eldritch god awakens, and another gullible soul is lured to the dungeon...
In Paper Mario: Color Splash, you first encounter a train called the Sunset Express in an early area called Marmalade Valley. It's held up because it's prepping for its final voyage, and because some archaeologists are using it. The next fifteen or so hours of gameplay conspire to make sure the Sunset Express won't reach its final destination. First, Mario has to break the tracks to progress the story, which peeves off the conductor. Then you have to gather up the twenty-four Blue Rescue Squad Toads to fix the tracks, a task that spans several areas and pretty much all of the next two "chapters" of searching for both the Blue and Purple Big Paint Stars. After the monumental effort of hunting them down, and after the Toads use their own bodies to make new tracks for the train, what happens? A Thwomp falls from the sky out of nowhere to crush the train. This is, of course, Played for Laughs.
In West of Loathing, this trope is lampshaded by putting a Shaggy-Dog Story, with an actual shaggy dog in it, inside a location called "Shaggy Dog Cave". The elaborate and detailed story is engraved on a long series of plaques, spaced out within an otherwise featureless cavern. As expected, the story ends with the characters finding what they were looking for, taking it, and leaving. To make the point even firmer, the shaggy dog in the story is a meaningless detail. And to top it off, the cave itself has no payoff—after all, they already took the treasure save for an El Vibrato monolith that can't be seen without a special item, which itself can only be used once per game.
The Necromancer sidequest requires you to travel all across the West investigating undead activity to locate the Necromancer's tower. When you finally find the tower, you climb your way to the top, facing a series of increasingly difficult encounters with the Necromancer's undead minions, until you see that the Necromancer himself has become so weak and decrepit from the use of dark arts that he's no longer capable of moving from his chair, and disintegrates with a single touch. Subverted if you have Doc Alice as your partner, in which case she'll shoot the Necromancer herself or if you learn all seven Nex-Mex skills, in which case you can choose to take the Necromancer's place.
In Assassin's Creed: Syndicate all of the player's actions revolve around discovering the location of a powerful artefact before the evil Templars can get their hands on it. The end cutscene shows the assassins acting on this information, but they arrive too late and take serious casualties whilst allowing the Templars to escape with it.
One sidequest in Xenoblade Chronicles X ends like this: A Nopon merchant sells a woman a lotion that causes her hair to fall out, so she forces him to go gather ingredients to make a cure. The Nopon ultimately manages to somehow strand himself on a floating island, necessitating the player character rescuing him and collecting the ingredients for him. By the time you get back the woman who lost her hair remembered that she's currently using an artificial robotic body, and simply got new hair from the maintenance center, ultimately rendering the entire quest completely pointless.
In the Super Robot Wars X verse, after Lelouch enacts his Zero Requiem in his world, rather than the world obtaining peace, the Mariemeia Army rises up and makes another attempt to go to war.
Leisure Suit Larry 5: Passionate Patti Does a Little Undercover Work: Pretty much everything that Patti does amounts to nothing. She shoots the villain, but despite drawing a gun in the White House in the presence of the Vice President, he gets off through a convoluted Chewbacca Defense. The mob's plan to use subliminals in music falls apart not because of her efforts, but because nobody could figure out to play CDs backwards. The mob's efforts to influence the government failed when their proposed bills got stuck in committee. And both of these together cause the mob to get out of the porn business, but that doesn't mean much because they quickly find alternative ways to make money. At least she got a weekend with Larry at Camp David out of it.
Valkyria Chronicles 4 has a comedic example - during a flashback, the real Kai deserts, having his sister Leena take his place. Nobody's going over the paperwork closely enough to notice the obvious difference, but eventually "Kai" is called up for a marksmanship demonstration. Clade and Raz, knowing Leena can't hit the broad side of a barn, sneak into the field and make simultaneous shots to create the illusion she hit... and afterward, it turns out Leena is actually a crack shot. She'd just trained with ironsights, and so didn't recognize the scope on her military rifle had been intentionally misaligned. Once a squadmate fixes them she effortlessly lives up to her new reputation.
One of Goro Majima's side-stories in Yakuza 0 is a comedic example. Majima meets a boy who has a "bag phone" (a very early version of the cell phone) who offers him to use the bag phone instead of a pay phone. Except the bag phone has a very short battery life, so Majima has to run to the store to get some more batteries. Then, lugging around the heavy bag phone hurt the boy's shoulder, so Majima has to get him some medicine. Then some punks attack the boy, and Majima has to fight them. Then it turns out the punks broke the bag phone when they attacked the boy. So he has his mom buy him a new bag phone. Finally, Majima gets to make his phone call... but he forgot who he wanted to call.
Claire's situation in Resident Evil 2 and in the remake. She went to Raccoon City after not hearing from her brother for some time and unwittingly got stuck during the zombie outbreak. Afterwards, she found out that Chris had already left weeks ago, leaving behind either a diary or a strange letter detailing his leaving or "vacation" to Europe. Meaning Claire traveled all the way here and was trapped in a highly dangerous, zombie-infested zone for nothing.
BattleTech: Used as a motivation for the villain, interestingly enough. Victoria, basically from the onset, has to win. If she doesn't, she has betrayed her cousin (who was her sister in all but name), assassinated her mentor and orchestrated a massacre of civilians for nothing. At the end, when it becomes clear that she has lost, she goes into a Villainous BSoD at the knowledge that generations to come will know everything about her misdeeds, and nothing about the goals and ideals that drove her to them.
This Is the Police: No matter what you do, what choices you make, who you side with, the ending is the same. Jack loses his job, off-handedly discarded by either Chaffee or Rogers, fails to reconcile with his wife, fails to make something out of his connection with Lana, is banned from his favorite club, and fails to change anything in the corrupt system. He at least gets to keep the money he made for himself, but it gives him little consolation as it was never about the money, while everything truly important to Jack was taken from him.
Because the game didn't sell well enough for the planned trilogy to be complete, this is the ending for XIII. The main character struggles to get his memory back and stop the other 12 conspitors whom are trying to over throw the United States government. He succeeds in doing this, only to discover in the end that the President (who took over after the other one was assassinated) is number 1, he has the main character in the middle of the sea on his giant cruise ship and he's surrounded.
The main plot of Creature Crunch is that the protagonist Wesley has been transformed into a half-boy/half-creature by Mad Scientist Dr. Drod and is guided by a Brain in a Jar named Brian to journey through Dr. Drod's mansion to find a way out and return to normal. At the end of the game, Wesley finds a way out of the mansion, but realizes that he failed to find a way to return back to normal. Brian then reveals Wesley actually had a monster costume on that he could've removed all along.
While this sort of thing tends to happen during the endings of Far Cry games, its not just limited to those. Case in point, the ending to the Kyrat Fashion Week questline in 4. After hunting down several different unique animals, Mumu Chiffon asks Ajay to head to his work shop and start the event off proper. But when he gets there, the workshop is in complete ruins. A note explains that Pagan Min, the games main villain, found out about the event and ordered his army to put a stop to it, and that Mumu has fled the country, rendering everything you did completely pointless. Its also got a slight Plot Hole, as one of the events requires taking Mins fortress, so unless the player sequence breaks, Min should logically be out of power.