AC2's playable credits sequence wasn't that crazy, but the ending had the holographic "ghost" of a pre-human being somehow knowing that in 2012, Desmond Miles would use an Animus to see Ezio's memory of meeting her — and therefore using the Flying Eagle of Florence as an answering machine to the future.
ACB ends with Juno taking control of Desmond's body and forcing him to stab a paralyzed Lucy, then in the post-credits we're left wondering if Desmond even is the player character... or whether he himself is an ancestor called up through a future Animus.
ACR involves a situation of *deep breath* Desmond entering Ezio's memory of entering Altair's memories. And that's before Ezio tells Desmond to listen to Jupiter.
Call of Duty: Black Ops: Most of the game, ESPECIALLY the penultimate level where it's revealed that Victor Reznov's been dead for years and the last cutscene at the end of the campaign which implies that Mason participated in or committed John F. Kennedy's assassination.
Cryostasis: Sleep of Reason lives on this trope. Filled to the brim with symbolic meanings, philosophical subtexts, biblical quotations, metaphorical Russian Folk tales, and a main character who is dead the entire game but eventually saved through winning a fight with the God of Time. Think Bioshock and STALKER combined and then directed by David Lynch.
Final Fantasy VII, the memory fuck-up part. Cloud finds his entire history is a lie and proceeds to angst for a good portion of the game. Followed by a trip into Cloud's subconscious where the player has to talk to various spectres of Cloud representing fragments of his past while a giant Cloud writhes in anguish overhead.
The climax of Final Fantasy VIII. First Time Compression occurs, the villain attempting to squeeze all of time and space into a single point and getting a good ways into it before the heroes abort her attempt. Then for the ending, Squall has his life flash before his eyes as it all gets put back... and then somehow Rinoa finds him and a desert landscape explodes into a flowering field. The ending helped popularize the infamous "Squall is Dead" meme, which states Squall actually died at the end of the game's first disc, the subsequent Kudzu Plot is his mind making up a fantastic adventure in its final moments, then in the ending finally completely breaking down. The ending's timeloop of Squall being the legendary seed who persecuted Ultimecia as a child, causing her to become the monster she is, and Ultimecia being the Sorcerress who gave Edea her powers, AND caused the events leading Squall to become the Legendary seed who persecutes her in the future. They truly were meant to battle each other for eternity.
The LOST videogame Via Domus, true to the TV show it's based on, features a major mind screw at the end. Throughout the game, the main character, Elliott Maslow (a survivor of Oceanic Flight 815 who has never been seen on the show), who is suffering from amnesia, has been trying to retrieve his lost memories. It turns out that Elliot used to be a journalist who ratted out his girlfriend Lisa, also a journalist, and took a photo of her being shot in the head by the guy the two were after. On the island, he is repeatedly haunted by visions of Lisa, eventually making him regret his selfish ways. The game ends with Elliott leaving the island on a sailboat, only to witness Oceanic Flight 815, the very plane he had crashed with, break apart above his head. Suddenly Elliott wakes up on the beach (instead of in the jungle, like he did in the beginning of the game) amidst the burning wreckage, when suddenly Lisa comes running towards him, relieved that both of them survived the crash. It should be pointed out that this ending was explicitly suggested by Damon Lindelof, one of the show's executive producers/main writers, and the concept of time travel had already been established on the show by the time the game came out. Fans of the show are torn whether this ending is really bad, or one of the few things that are actually good about the otherwise critically panned game.
Several works by developer Goichi Suda (b.k.a. "Suda51"). The extent of the weirdness depends on how seriously the game tries to take itself:
Killer7 stands to define Mindfuck but it becomes 'a little' easier when you realize most of the plot elements are supposed to be disjointed. It's all just Harman Smith and Kun Lan playing chess with the world. Emir Parkreiner killed the Smith Syndicate and after he thought he killed Harman, suppressed the memory and became the entire Smith Syndicate in his own mind. All the ghosts were people Emir had killed and in the end he was just the chessboard, the Heaven Smile were Kun Lan's pieces, and the ghosts were Harman's pieces (except for Iwazaru, who apparently was Kun Lan trying to fuck with Emir to mess with the game but in fact he was helping Emir not remember who he was to keep the game intact? And the bosses were actually Harman's pieces to develop Emir's fake identity and keep him from realizing the truth.
The plot of Contact is largely ambiguous and open to interpretation, especially the Professor's and Mint's motives. The ending is pretty confusing as well, and probably creates more problems than really solves any; there's a divide amongst those who've played the game as to whether it was really unique or just anticlimactic.
Chapter 5 of Kid Icarus: Uprising takes Pit to Pandora's Labyrinth of Deceit, a bizarre place filled with moving walls, fake tunnels, and passages that are actually much longer than they appear. Chapter 21's Chaos Vortex is even more screwy, and pretty frightening as well.
Dreamfall: The Longest Journey. The ending. Well, calling it an ending would be a bit of a stretch, the thing practically ended midway through act II.
It's been twelve years, and The Stanley Parable has taken another stab at it. A narrator tells you what to do and everything that you're doing (the game demonstrates a clear hatred towards linear video games), even though there are obviously other choices. If you follow everything he does, Stanley turns out to have been under mind control and frees himself, but you still wonder if he's actually free. If you defy the narrator at any point, he attempts to bring the story back on track or find a new one, and he repeatedly states that it's just a video game. As you progress, you begin to wonder if you're Stanley or someone controlling Stanley, if the narrator is the designer, or if the narrator is just another character. It's so extreme that one of the first Let's Play videos of the HD Remix was called "The Stanley Parable - A Story About Mindfuck".
At the beginning of Sanitarium, you wake up in a mental hospital with no memory and bandages wrapped around your face. Flashbacks appear sporadically as you play through the game and alternate between roaming the grounds of the hospital and going into bizarre settings where you actually seem to be other people, to the point where it's unclear what's real and what's delusion. Turns out that it's all delusion - more specifically, it's a big dream you had while you were in a coma after your car wrecked because your evil business partner cut your brake lines. However, the symbolism of the settings and actions during the dream is still of great note.
Silent Hill 1 screws with the player by taking things a step further than simply having a confusing plot: the game has no third-person narrative; it's played entirely through the point of view of the Player Character. Because he's kept in the dark over what's going on, the player is never let in on things either. It isn't until Silent Hill 3 that the full story is finally revealed.
The game screws with you more in Silent Hill 3, where it's suggested that the monsters you've been killing may be innocent people, and all the dangers you've faced are all in your head.
Silent Hill 2 gets really mind-screwed in its second half, with the stuff that goes on in the Historical Society Abyss and the Hotel.
Shadow Of Destiny is a more mild example than some on this page, but nevertheless tends towards this. The game is designed so that you have to play all of the Multiple Endings to know what's going on, but at least two of said endings directly contradict each other; the ones that DO let details slip don't explain what they mean; certain details are revealed and then re-revealed as something completely different; and the only character who knows what's going on refuses to enlighten the rest of the cast. Lampshade hung when one character admits that The Reveal she's just given you is based on things she's been told and that "not all of it may be true". Its Spiritual Successor, Time Hollow, falls squarely under this too. Don't expect to understand the real motivation behind anything or anyone until the epilogue, and it's a bit iffy.
Earthbound: Children with giant heads attacking wildlife everywhere, possessed street signs, a glowing neon Dark World of backwards talking shadows, talking dogs, an afterlife that looks like a Grateful Dead album cover, and the final boss (Whom you, the player, not the characters you are playing as, have to fight). Its predecessor, for one thing, had you entering someone else's mental world, by... touching a seashell and reading a diary? And then came Mother 3, which is even stranger.
The ending of The Final Fantasy Legend (aka Makai Toshi SaGa) — You've been climbing up a tower that leads to various worlds. You fight the Big Bad. And then you walk through the door that leads to the top of the tower... only to fall through a trapdoor all the way to the first world at the bottom. You pull yourself back to the top, the door to "paradise" opens, and... you're in a featureless white room. Wandering around leads you to The Creator of the World, who says you've won "the game"; you promptly decide to fight him. You discover a door behind him but decide not to investigate and to go home instead. The Gameboy equivalent of Neon Genesis Evangelion, that ending was.
SD Snatcher is probably the closest to examining the innards of Hideo Kojima's brain most people would like to come. The plot's perfectly straightforward (if a bit odd) until about halfway through, where it begins a slow downwards slide - starting from Gillian being forced to pretend to be Solid Snake in order to clear his name after killing a priest and ending with Snatchers in fursuits and clown suits colonising a ripoff of Disneyland (hidden behind a painting) because it looks like the Kremlin. Actually, no, it's probably when the master Snatcher manifests out of a pool of liquid skin.
Don't Eat the Mushroom and Carousel. The former because it's a drug trip and the latter because of its Gainax Ending. To play these two, though, you'll need to download Knytt Stories, a fun platforming game you can make levels for. For those who can't access the linked forum, there's a video LetsPlay of Don't Eat the Mushroom on this page (scroll down a bit to find it).
Second Sight's last few levels, though not as bad as most of the entries on this page, was still rather mind-screwy. Mutant kids eating the Big Bad! The present is the future! The past is the present! Jayne's dead! Jayne's alive!
The Xbox Live Arcade Game Braid has a highly confusing story to go along with it's tricky time-manipulating gameplay. Absolutely everything is metaphorical. What appears to be a simple tale about rescuing a princess turns out to be a complex story of a man's obsession, and the atomic bomb, or something. After playing World 4, in which the timeline is controlled by your position in the level, a friend of this troper was afraid to scroll through chat logs, for fear that he would undo the most recent messages.
The entirety of Mondo Medicals and its sequel Mondo Agency. Unless you have a complete understanding about CURING CANCER BY SHOOTING PEOPLE WHILE THINKING LIKE A STAR or how killing indians in order to save technology will somehow save the president... before you kill him, then you're screwed with these games.
The little-known Baroque, which takes place in a distorted world where people physically transform into a metaphor for their twisted delusions. It's confusing enough from the very start that, by the time you learn that the flying babies with deformed faces are actually the physical manifestation of God's pain, and you've been firing them out of your Infinity Plus One Gun, you'll be relieved that the plot is starting to make more sense.
The Elder Scrolls series retconned five of Daggerfall's conflicting endings into a single canonical event by making it so that they all happened at once, breaking the relationship between time and reality and causing all sorts of incomprehensible chaos.
Anything written by Michael Kirkbride. 36 Lessons of Vivec is an excellent example.
Most of the "background" stuff is actually this, and it does bleed into the main games occasionally. An example: Alduin is Nord-Akatosh and is the firstborn son of Cyrodiil-Akatosh who was created by St. Alessia long after he started existing. Cyrodiil-Akatosh is also Auriel, who is Alkosh, who is the Aka-Tusk, who is Bormahu. All of these beings exist independently of one another, while simultaneously not being distinguishable from each other. And the denizens of Tamriel are okay with that. Talos is three humans who became one god, and is also Lorkhan, who is also Akatosh.
And there's CHIM. In one way it is the power granted to those who understand that they're living in a video game. It can also be understood (again, given a hyper-simplified, bare-bones explanation) as an in-universe realization that the Aurbis is merely the dream of the Godhead. Both of these interpretations are equally true, and each interpretation serves as a metaphor for the other.
Sheogorath is the physical embodiment of the Mindscrew. Not surprising since he's the Daedric Prince (A lesser god in that universe) of insanity. He speaks complete nonsense at times, his plane of existence is divided into two halves representing himself. "Dementia and Mania" and he enjoys nothing more than driving people insane, or playing with people like they're toys for his amusement, or just plain playing sadistic pranks on people. His signature items are a staff that causes four scamps (goblin like creatures) to follow the holder forever unless he/she places the staff in his shrine. The second is the Wabbajack which can turn any living thing randomly into anything from an bunny to an unholy demon. Not to mention the fact he speaks with an accent that sounds both Irish and Scottish at the same time and is the only character in the fourth game who has facial hair.
Interactive Fiction work Shade. To avoid unnecessary spoilers, it starts getting weird fast, and ends with one of the most cryptic, incomprehensible scenes ever seen. How did the tiny human figure crawl out of the sand if it's dead, and what did it mean by "You win. Okay, my turn again"?
Fortunately, a combination of Word of God on the official thread and Guide Dang It clues make it far more comprehensible. The fact that the Player Character changes without any ingame indication adds to it. One interpretation is that the player character already went to the event in the desert, and is, in fact, one of the persons whom the radio mentions going missing. As the player character suffers the effects of dehydration, he begins to suffer from psychosis and hallucinates that he is back in his apartment prior to leaving. As he dies, he begins to see through portions of his delusions, and portions of his "apartment" turn into the sand that is really there.
Star Ocean: Till the End of Time involved a massive Mind Screw late in the game. It was revealed that the entire universe was, in reality, a MMORPG for 4D beings, thus making all the characters computer programs that happened to gain sentience. If that wasn't enough, the Big Bad succeeds in deleting the entire universe. It no longer exists, but it still happens to exist because people still thinks it exists even though it got deleted. Is your head splitting open yet?
Let me put it this way. If you make a bell through a mould, the bell isn't affected by the mould's destruction, so long as casting is complete. Lucifer only destroyed the mould; nothing happened to the accidentally-created bell. Better still, Lucifer had no idea any casting had happened, and dismissed out-of-hand that any casting could happen; he only knew of the mould's existence, not the bell's. To be honest, you'll have a slightly better idea of what's going on if you're familiar with Gnosticism.
However it REALLY gets bad when you consider before attempting to delete the universe entirely, Lucifer sends the Executioners to manually delete the inhabitants of the Milky Way, including whole civilizations, ships and Earth itself. It is specifically said that these have been deleted. Yet the universe still exists when it is deleted? The implication is that the inhabitants of Earth and such didn't think they existed!
Both F.E.A.R. and Project Origin's hallucinations are generally chaotic mindfucks that in a lot of cases don't make a whole lot of sense at first glance... or even after you've got the proper context. And in Project Origin, there is a literal case of a Mind Screw, where Alma rapes Becket during a hallucination.
What makes you belive it's a hallucination?
LSD: Dream Emulator was an early PSX game based on the dream diary of a real woman. This is important to know because the "dreams" you can have in the game are insanely absurd. The game itself is very open and you can interact with nearly anything, but the more you interact with things and the more dreams you have, the stranger the dreams become. The limited edition book that came with the game is a copy of the woman's own dream diary. Fans still endeavor to understand what it all means, though.
Chu-Teng, Tong-Nou's sequel, makes just as much sense, and was only realeased in Japan.
An earlier Bungie series, Marathon, certainly qualifies as this, to the point where a fan community sprang up around trying to decipher its story. The entirety of the story is told through a series of text-based terminals, many of which are extremely cryptic and full of mythology references. It didn't help that many of the terminals were in hard to find locations and easily missed.
Marathon Infinity, when jumping between different timelines in order to find the one where the universe can still be saved from the W'rkcacnter, you go through very strange "dream" levels. The terminal messages found on Where Are Monsters In Dreams are perfect examples of this.
Three of the many fan-spinoffs are even stranger, in order;
.flow's ending has one of the creatures from the dreams, a chainsaw-wielding maid, pop up in the real world. The implication is that she kills you. Even before then, going to certain parts of the dream world too often, and triggering certain events, leads to your "real" room rusting, and eventually, an IV monitor showing up.
LCD DEM is pretty standard Yume Nikki-spinoff fare until its ending, which has Chie exiting her room to find what appears to be her mother, dead and bloody on the floor. This happens with zero foreshadowing on even a symbolic level.
Answered Prayers is unfinished, so it's mindscrewiness may be at least partly because of that. But it has a short text opening that is difficult to explain, and the very method by which you enter your "dream world" is odd, as it involves you praying in a temple instead of going to sleep.
Vampire: The Masquerade – Bloodlines: The coffin is a mindscrew. The player is filled with legend speculating on its contents, is given a life-threatening mission to recover it, and the one character who begs you not to open it is acting pretty out of character... who wouldn't open it?
Playing as a Malkavian turns the entire game into a mind screw, your character has an almost frighteningly good grasp of what's happening and what will happen, all the way to the end of the game, but they hide it in flowery metaphors and fourth-wall-breaking comments confusing enough that you won't realize it until a second playthrough. It's still a Mind Screw when Caine himself shows up. Cue the freakout.
Vagrant Story, particularly the ending; though most of the game involves the protagonist trying to figure out what in his head is real and what isn't.
The whole WORK of Tetsuya Takahashi would apply for it. While Xenoblade is slightly more straightforward, Xenosaga ramps the Mind Screwing Up to Eleven.
A lot of The Path has this; for example, pictures and patterns randomly flashing over the screen, the random items you find littered around the woods and anything you see in grandma's house after encountering the wolf, especially if you've unlocked the secret rooms.
Actually "unlocking" anything is a mindscrew in itself. The lit up items in your inventory don't seem to be the ones that are counted at the end of each stage, and when you don't unlock anything, you'll still see the same scenery (but unlocking does let you know about it in advance). There are collectable gold clovers in the game— What happens if you get them all? Nothing. Absolutely nothing. The entire scorecard and "game" features of the game seem to be there shearly to mock the concept of a traditional game, something which The Path is most definitely not.
There's a fairly minor one in Baldur's Gate- in the catacombs under Candlekeep, you meet Elminster, Tethoril and your stepfather Gorion- who was murdered at the end of the prologue. They tell you that Gorion was actually poisoned and made to look as if dead, and that for some time you've been trapped in a grand illusion created by the Big Bad and his doppelganger minions- and you've just murdered most of your childhood friends, believing them to be doppelgangers. If you believe them and follow them, they lead you past a load of apparent Doppelgangers, who chase you- and the three characters turn into Greater Doppelgangers and, if you aren't careful, kill you. Bastards.
Tales of the Abyss makes perfect sense right up until the ending, at which point it suddenly enters full Mind Screw mode and refuses to explain what happened.
Two of the bosses in the VIP 5 Super Mario World hack are complete and utter 'what is that' things, such as Tanasinn and Julius. The first has some weird quotes too, such as Don't think. Feel and you'll be Tanasinn. and I lose. However, I am immortal. Anything can become Tanasinn. You are also the same.. It's the strange embodiment of Japanese Message Board memes...
You get little (was that a gas leak I just walked across?) to no warning at all that you've received a facefull of scarecrow toxin. Especially the fake game crash glitch and fake game reset that turns into a modified version of the intro cinematic where a very serious Joker is driving the insane Batman to Arkham. These sequences are made worse by the But Thou Must factor being in effect. Even if you know where the gas is, you can't grapple to avoid it (if you do, you still get gassed), there are no passages around it, and the door you entered that corridor through locks behind you. Nighty-night, Bats...
Dear Esther, a mod of Half-Life 2, is famous for this. You're walking around an island all by yourself, and there is no gameplay. The entire story is told through narrated letters, and you won't hear all of the letters in one playthrough, meaning your understanding on the plot changes. Not only that, some of the letters contradict each other; sometimes the narrator was shipwrecked on the island, other times he is a hermit seeking solitude. At the end you turn into a seagull and fly over the letters, which shouldn't be on the island.
Another Half-Life 2 modification, Korsakovia (made by the same minds behind Dear Esther) is one big mind screw. At first you think you are simply experiencing things in a screwed mind, while hearing your neurologist, Dr. Grayson, talk to you, but then things get weirder and weirder, until eventually a chapter title reads "The Assimilation of Dr. Grayson".
Kingdom Hearts: Chain of Memories? Try the opening for the first game. And that's not even touching any of the other games, or the infamous "Snarl of Memories" cutscene from 358/2 Days.
Would the fact that memories of Sora and Xion magically disappear and with memories of Sora magically coming back without explanation count?
The first time Axel, Roxas, and Xion sit on the clock tower. At first you think the hood thing might be a silly developer error you caught. Then it happens again, and again, and again... but it gets explained when it's revealed everyone sees Xion differently and the hood being up is the game not trying to reveal that until later.
Condemned: Criminal Origins had a pretty standard "Clear My Name and catch the serial killer" plot. But it also had all the homeless people go crazy and mutate, and the main character hallucinate for no adequately explained reason, which made the whole thing creepier. Unfortunately, they explained it in the sequel.
Said sequel runs out of plot after about three levels, though. It starts off as a horror game but suddenly you're fighting animated suits of armour and figures made of black goo, and you cure Ethan's alcoholism by fighting the living incarnation of it, and you learn he has the ability to make people's heads explode by yelling at them really loud. And aliens are behind it all. Maybe.
The scene in The Legend of Zelda: Twilight Princess where Link is supposed to learn what happens when the powers of the Fused Shadows are abused... It ends with an army of giggling clones of Link's best friend Ilia, falling from the sky. And that's just how it ends.
The ending of Mystic Ark. Nowhere in the game does it tell you exactly what you're doing or why you're doing it until right after you beat the final boss, and then the end of the credits only makes it all the more confusing.
Planescape: Torment, where the whole storyline is one big mind screw. It does get explained, however, but it's certainly screwy for the bigger part of it...
The ZX Spectrum one-arm-bandit simulator Dizzy Dice has a mode where you try to earn as much money as possible, beating four successive targets. Beat the last target (and hence the game), and the result is a fake "system reset".
Alan Wake gets more and more screwy as things go on. It's not long before other characters think that Alan is crazy, and he's not only admitting the possibility, but saying it might be a good thing: "It takes crazy to know crazy." Then the ending tops it all.
Even more so in the sequel where the old city is an hallucination induced by the vapors of a rare ore that Pandora's Box is carved from. It makes the affected person extremely suggestible and it just happens that the first thing you see getting off that train are pictures of that old town. It also explains the coma of those who handle the box as the story of the "curse" has them expecting this to happen.
Rule of Rose: Probably All Just a Dream, but even then raises a huge number of questions in the vein of what actually happened and in what order, as the chronology is severely muddled up. It has served as fan fodder for five years and counting!
The game does make perfect sense if you view it through dream-logic and child-logic simultaneously. Assuming that you've found most of the semi-hidden plot points (the game lets you skip ridiculous amounts of exposition without realizing it). Yeah, it's not easy...
The Secret Level in Batman Doom. It's called "No Comment..." and "Weird!", and both names fit. Imagine Batman on a giant island made of flesh, floating in the middle of inky blackness and with biting mouths in the ground, with clock-adorned trees taken right out of Dali's "Persistence of Memory"; Batman must fight against floating eyes that throw batarangs at him and that leave the eyeholes of a giant mountain made of meat. Once you beat the eyes, you can enter the mountain's toothy mouth and proceeds down its... digestive tract? to the room with the exit. And the level music? The cheesy theme of the Batman TV show.
Parts (especially before the players get to the Answer/Core arcs) of the When They Cry series can be summed up neatly as Mind Screw: The Game.
Deadly Premonition does a good job of tying up most of the plot threads by the end of the game, but there are still quite a few other questions that are never really answered. Like, how much of the action sequences were actually real? What exactly are the Shadows? Why could Emily see them? How much of Harry's story was true? What did the military have to do with all this? Why was Kaysen in the military at all? Did the final boss fight even happen? Why does everyone intuitively know to call you Zach after The Reveal? Does that mean that you only thought you were calling yourself York? Why can Isaach and Isaiah see dead people? Why were they in the Red Room? What was the Red Room? What did Kaysen mean when he said that he was from the "Red World?" The biggest remaining questions revolve mainly around how much of it was meant to be taken as occurring, and how much was meant to be symbolic representations of the events of the game.
Chrono Cross has some particularly Mind Screwy moments, especially compared to its rather straightforward predecessor Chrono Trigger. The Dead Sea, in particular, is left almost completely unexplained, to the point where severalarticles have been written by fans trying to explain exactly what it is.
Pirouette is one of the most Mind Screwy web games out there. The game stars a presumably female character with multiple wives — one of whom died twenty years before she was born — as she meets the wives in the final seconds before they die while half-heartedly warning them of their impending doom. The bizarre, vaguely written Purple Prose seems to imply that all the relationships may have been toxic, and the dialogue about screwing is screwy — "intercourse" is used to refer to both conversation and sex, often only a few sentences apart. To demonstrate just how bizarre the game is: at Jay Is Games, which features detailed reviews and comments on web games, Mind Screw art games are fairly commonly featured, so the people in the comments are usually savvy enough to properly interpret such games and come to a consensus on said interpretation. With Pirouette, the people in the comments had no clue what was going on, and the interpretations that actually sprung up were more humorous, half-hearted attempts to sift out some sort of meaning. To quote one person:
Echoloco:Okay, if I'm interpreting this correctly (which I highly doubt) then, taken at face value, with as little induction as possible, the main character is a she-male and/or transgender and/or imaginary friend with benefits who is also a time-traveler and/or dimension shifter and/or a necrophiliac and/or a polygamist and/or a lesbian and possibly the last of his/her/its kind. To be honest, I'm not sure if he/she/it/they is/are human. Trippy.
The freeware game A Mothers Inferno has some incredibly trippy visuals and unusual creatures.
EYE: Divine Cybermancy starts off in a trippy dream world full of pillars and a gate of light, then you go through it and wake up in a cavern with no memory of anything. You fight your way through monsters and a civil war until the time comes to kill your evil boss Rimanah, after which another gate appears where Rimanah, Your Mentor, and Mysterious Person all deliver peculiar lines of dialog before sending you back to the start. Characters scattered around deliver dialog relating to other events that don't seem relevant until you get all three endings, go back to the tutorial again and find a gateway leading to a labyrinth. If you fight your way to the end of it you get to talk to a woman in white then step through a final gateway leading to a bizarre place where you earn the achievement Rimanah's Dark Secret. The game pretty much leaves it up to you from there to figure out what the hell just happened and how much was real.
The Halloween Hack: Varik is the main character of the story. He is joined by Jeff, Paula and Poo - but not Ness. Where is he? The game often draws strange parallels between the two, as if they're the same or Varik has replaced him in more than a story role...
Reality On The Norm has some games like this, especially Nihilism, Davy Jones C'Est Mort and Surreality, which are basically Dada in video game form, with no plot to speak of and bizarre characters in strangely drawn locations.
Games by Tobias Schmitt used to feature this heavily too (usually featuring the characters exploring strange environments while philosophizing), but later were all removed from the site.
Singularity is not quite as bad as many other cases, but has its fair share of Mind Screw and Paranoia Fuel mixed in together due to hidden messages that can only be revealed with the Time-Manipulation Device. They'll tell you not to trust some person or another until finally telling you, "Don't trust me." You can also find the mysterious messenger's attempt to diagram the time loop you've just intruded into. The messenger is the player character, Renko, having gone through countless iterations of the time loop. In fact, the nature of the time loop can make one question whether the "base" timeline that resembles the real world is in fact the base, or just another warped iteration. Maybe the original timeline looked nothing like modern Earth?
While the varied stages in McPixel are frequently off the wall (and, sometimes, have solutions fitting into this category), the real examples are the bonus stages you reach for solving three puzzles in a row without failures. They include a room full of McPixels, standing on a rainbow of a cow pretending to be the NyanCat, and a stage deliberately designed to resemble a glitched out level.
The ending of Bioshock Infinite features the "sea of doors", an ocean filled with lighthouses, each representing a potential parallel universe adhering to the basic template of the Bioshock storyline. The quirky seemingly omnipotent twins who appear around Columbia to give the player advice also count, at least until you find out what their deal is.
Perhaps the sole example among (semi)realistic tactical military shooter, which typically are very clear-cut, is Spec Ops: The Line. Not only is it unique in said specialized subgenre, it generally boasts more Mind Screw material than most other shooters, hell, than most other games.
While quite coherent in its main narrative, Max Payne 2 contains a fair amount of mind screw: the prime examples are Max' dream sequences, throughout, and the in-game TV showAddress Unknown. It also manages several chronological leaps, a few instances of... interesting symbolism and several NPC conversations (on which you can eavesdrop) that are somewhat surreal.
Fire Emblem: Sword of Seals has a small one in a support conversation between Treck and Gonzales. Over the course of their discussions, which never progress past introductions, Treck takes his tendency to forget other people's names to a new level and by the A Support, forgets his own name mid-conversation and when Gonzales erroneously tries to remind of his name, assumes that the name Gonzales gave him was correct.
Occurs a few times in The World Ends with You. First and foremost, to play the Reaper's Game, you have to be dead. Shiki had her appearance taken as her entry fee, and takes on the appearance of her best friend Eri. Neku was killed by Joshua. Hanaekoma is not only CAT, but is also an angel. The last, and probably biggest Mind Screw is that Joshua is the composer, and the three Games are part of another Game between him and Kitaniji to determine the fate of Shibuya.
The entire battle with Tigris Cantus (aka Mitsuki Konishi), a thoroughly bizarrePuzzle Boss.
Quest Fantasy, especially the first one where things are not nearly as explained as they are in later entries. One particularly memorable example, though:
You open the chest.
You were inside!
The Last Door has wall-to-wall mindscrew. It's in every Chapter and in scene after scene. Here's an example from Chapter 3: after falling out of the coffin you were buried inside of in Scotland, you find yourself in a London slum with a ticket in your pocket. A man with a red beard and a cape appears to lead you around the city. After solving a slew of puzzles, you find yourself wandering through a misty forest filled with the sounds of cicadas, crows, ocean waves, rushing wind, and (somehow) silence. Through the mist you find a manor house at which the man you've been following asks for your ticket. When you turn it in and step into the house, the camera pans to show four statues that represent you, two friends, and your old teacher. The inside of the manor is a theater and a school friend is on the stage. He babbles about finding answers about the Bird that has taken you under its wing and then raises the curtain to show you a group of people in expressive white masks all laughing and crying. Your friend holds out a mask and tells you it's yours. Even when you have the context of plot, it makes precious little sense.
Pretty much everything about Gingiva, which is mostly a social commentary buried under very bizarre metaphors. This is entirely what the author intended.
The trailer for Antichamber starts with a quote from a critic saying "Even as the developer told me what the game was doing to mess with my brain, it still succeeded in messing with my brain."
In Robopon, Illusion Village is this on purpose. Its inhabitants all speak backwards or in roundabout ways, and the village itself vanishes at times.
Video Game/OFF starts off as mildly quirky and a little unsettling at times, and begins a slow descent into madness until the end, which becomes full-on bizarre, confusing and horrifying (it doesn't help that the English translation initially misinterpreted and mistranslated the relationship between the Batter, the Queen and Hugo.)
The first playthrough ends with the Eld Witch killing Alice. After her defeat, Loue and the Wonderland inhabitants try to force Liddell to become their new Queen. The screen goes red, and then Liddell wakes up—the entire playthrough was a dream when Baba Yaga hit her on the head, but it's later revealed it was a test from Queen Alice.
The second playthrough ends with Liddell killing the Eld Witch, who is revealed to have been Anne and transforms into her as she dies. Liddell begs her to live, but it's too late, and she dissolves into ashes. Liddell works her way through the maze and is told that death isn't always the end. Then she meets the six princesses, who tell her that this was all a dream Queen Alice created on Liddell's side of reality, and it's time for her to wake up. They hope to meet Liddell in real life and bid her farewell. Liddell wakes up in her room and can't remember her dream, but she has Anne's bracelet with her. Loue is seen on the rooftop above her.
The ending of the videogame adaptation of Futurama, written by David X. Cohen, has the crew getting killed by Destructor, which leads to the events that begin the game, resulting in a Stable Time Loop in which the crew is dead.
Spore's ending: You zoom in to the planet, and then you get teleported to a new universe, receive the staff of life, and god offers you a timeshare in earth.
Winter Voices has battles which take place entirely in the protagonist's mind, traps like "Buried Sorrow," enemies like "Uncertain Mystery" and skills like "Betrayal." (Which, according to the description, grants you increased damage evasion abilities by changing your personality.) Even some of the Steam achievements have obscure, confusing names like "Genius Of The Mountain Pastures" and "The Only Water In The Forest Is The River."