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Silent Hill. The entire franchise is one huge mind rape for the player, focusing on reducing you into a state of complete fear rather than bowling you over with pop-ups and run-at-you monsters. The entire Silent Hill series is notable for its scene setting to convey the complete horror. It is for this reason it is often cited as the ultimate horror game series.
There's even a Does This Remind You of Anything? scene in Gongaga where Cloud's lying on a bed, clearly severely traumatised, while the others try to convince him that what Sephiroth forced him to do wasn't his fault and doesn't mean Cloud wanted it. Let's add into this the way Sephiroth tells Cloud 'I am always by your side', and the bizarre sexual symbolism of Cloud being forced to find Sephiroth's Materia coffin in the centre of a pink, pulsating, ring-shaped structure, and penetrating it to give him the Black Materia.
On a similar note, Final Fantasy IX had Zidane suffering a BSOD... not from finding out that he was an alien who was meant to be the Angel of Death for his adopted homeworld, but from actually having the man who created him rip his soul out. Fortunately, that just made him wangsty until his friends could give him a sequential pep talk.
Final Fantasy X-2 has Shuyin, who was trapped in a psychic prison and forced to relive not only his own death, but the murder of his lover... for a millennium. Understandably, on getting out, his only goal was to destroy absolutely everything just to keep that from ever happening to him again.
Somewhat dissimilar to the previous three Final Fantasy entries but, the second MMORPG entry in the series, Final Fantasy XIV, has an ability called 'The Echo', granted to anyone who witnessed a strange, meteor-shower like event at the start of the game's story (this includes player characters). The Echo allows the user to touch souls, granting the ability to speak to all sentient beings and enter and change their memories. The people on whom it's used without their consent - and are able to recognise someone invading their memories - have at times angrily highlighted the Unfortunate Implications.
Metal Gear Solid 4: Guns of the Patriots. Beauty and the Beast Unit. A group of four women, implied to have latent psychic ability, who were utterly ruined and destroyed by war crimes. Though the mind rape was unintentional, it was still quite effective. Now the only thing they live for is war.
In Half-Life 2 Episode 1, Gordon Freeman is mind-raped by a Combine Advisor in first person. It's not fun for him or the player.
This happens a number of times in Episode 2, as well.
In Kingdom Hearts: Chain of Memories Naminé is first ordered to make the clone of Riku think he's the real Riku (she also makes him devoted to her). Later on, she voluntarily breaks the links in his heart, basically snapping his mind and memories to stop him from attacking Sora.
There is also what she does to Sora, to a lesser extent, by removing and manipulating his memories.
And in the prequel Kingdom Hearts Birth By Sleep we have the creation of Vanitas, which leaves Ventus in a catatonic state and memoryless for quite some time. Then, just before the story's ending Ventus returns to the Graveyard, only to be confronted by Master Xehanort. Just a smirk caused his sleeping memories to return, the pain causing him to scream and collapse. It became so much that before the last battle he begs his friends to destroy him. If you didn't cry at the look of his face after that you have no soul.
Kingdom Hearts Dream Drop Distance features Sora deliberately being mindraped so thoroughly, his heart momentarily snaps, allowing darkness to invade it and leaving him catatonic until Riku rescues him.
In Drakengard there is a disturbing cutscene in which Manah begins to speak in her evil man-voice, speaking Furiae's innermost thoughts out in front of her brother, the protagonist. Okay, not too bad, unless you happen to be harboring incestuous feelings towards your brother. The allusion to rape is helped along by Furiae's winces and verbal reactions throughout the whole ordeal. Her shame is so great that she immediately commits suicide. Manah also does this to the Anti-Hero's best friend early on in the game, using it as part of the process for More Than Mind Control to make the best friend into a Rival Turned Evil.
It's also the function of the Secret Project known as the Dream Twister. It increases the strength of psychic attacks, and the video for it shows a mind rape in progress. (The same video is used for the Neural Amplifier, but with the attack broken up and defeated by the device of that name.)
Though it's not dwelled upon especially much in the StarCraftExpansion Pack, the Dark Archons have the ability to instantly mindwipe a creature, alternatively overload their nervous system, rendering them paralyzed for a short amount of time.
If you take into consideration the power that pretty much every individual of the entire Protoss race have in the lore, you could just as well say it's a race of mind rapists.
The final battle of EarthBound was, according to the game's creator, a replication of his own mind rape (a "direct attack to [his] brain," in his own words) he suffered after walking into a drama movie in the middle of what he thought was a rape scene as a child.
In Halo 3, before and after rescuing Cortana, her words and verbal cues drop indications that the Gravemind is inflicting this on her. Bear in mind, while an AI she's built off of a human mind, so she's just as vulnerable as any human. The rather agonized, audibly shaken way she begs for the Chief to get her out of High Charity and to destroy the reactors to pay it back just emphasizes this.
Cortana:I tried to stay hidden, but there was no escape! He cornered me, wrapped me tight and brought me close...
"Human Weakness", a short story in "Halo Evolutions", is entirely composed of this. And the dialog she uses is like something right out of Law and Order...
The Zuul of Sword of the Stars regularly perform mind raping of lesser beings to perform research, leaving their victim a maddened degenerate husk. In fact, they do this to obtain information in general... Or because they think it's fun... Frankly, the Zuul like mind raping their lessers and thus they never really got used to asking nicely. Or asking at all.
The PresterZuul use their Mind Rape abilities for more constructive purposes. "Sin Eaters" will help Liir soldiers deal with their guilt over having killed sentient beings by erasing selected memories.
Mass Effect: On Feros you discover a mind-controlling creature known as the Thorian. It works because its spores implant in your brain and cause agonizing pain if you even think something you aren't supposed to. Of course, at least one person intentionally thinks the wrong things in defiance. He says he's "Just invoking the master's whip."
Anyone who spends any amount of time around Sovereign and any other Reaper is automatically mindraped by its energy field.
Matriarch Benezia's description of indoctrination is particularly brutal: "His teeth at my ear! Fingers on my spine!" "I am not myself, I never will be again!" And, for added discomfort, Benezia is voiced by Marina Sirtis, who played the above mentioned Deanna Troi.
Let's talk about indoctrination a bit more. All Reapers can do it, even when they're dead. Certain pieces of Reaper technology are also capable of doing it. You might be able to resist it at first, but eventually you'll succumb. Your mind will become a tool for the Reapers. You will obey their commands without even realizing they are commanding you. And when they no longer have a use for you, you will be assimilated, either infected with Reaper nanites and turned into a hideous mockery of yourself or melted down into genetic paste to create a new Reaper.
The Prothean beacon mindrapes Shepard for two reasons: first, the transmission wasn't meant for a human mind and required an in-depth understanding of the Protheans to make sense of; second, the beacon was damaged and transmitted an incomplete vision that lacked concrete information until Shepard got the complete package on Virmire and realized the Conduit is on Ilos. It doesn't help that the message is also a warning about the Reapers and shows some graphic detail of the Protheans' extermination.Mass Effect 2 makes a callback to this in a sidequest where Shepard finds another copy of the message, this time with one added image: Collectors as the Protheans, because they're the same species.
Mass Effect 2: Morinth and other Ardat-Yakshis are compelled to commit mindrape. They court their prey and eventually brainwash their "paramours" until they have sex, at which point the Ardat-Yakshis' orgasms cause their "paramour's" brain to melt. So mindrape, in this case, leads to physical rape and murder.
In Knights of the Old Republic 2: The Sith Lords Kreia uses her mind invasion techniques in conjunction with Hannibal Lectures to inflict this upon the Player Character's companions, breaking them into his/her service. There's also the first game, where it is implied that Malak does the same to Bastila in order to gain an underling. And also possibly more conventional rape, judging by his suggestive dialogue and behavior during that cutscene.
In F.E.A.R., this happens to anyone who has had any lengthy contact with Alma, but especially the Point Man and Sergeant Becket. In the former case, its because the Point Man is her son, while in the latter case, its because Alma is apparently in love with Becket and repeatedly tries to literally rape him, eventually succeeding.
In Dawn of War 2, the cutscene that introduces the Tyranid creature called the Zoanthrope does this to the player: random and distorted visuals overlapping with the image of a bloated alien braincase, with loud screeches paired with the sound of audio feedback assaulting the ears.
This is basically a visual representation of the Tyranid psychic power 'The Horror', which is Mind Rape taken to the third degree.
Shadow Priests in World of Warcraft have many abilities made to mess with the opponents mind. These include Mind Blast (causing an explosion of shadow magic inside the enemy's brain), Mind Flay (slashing at the enemy's brain with shadow magic whips), Mind Sear (burns the opponent's brain with shadow magic) and the classic Mind Control. Both Priests and Warlocks can cast a version of the Fear spell, which causes immense fear in the target's mind, making them run around aimlessly for a few seconds.
Priests of any sort - Holy, Discipline, or Shadow - are expected to get Mind Blast and Shadow Word: Pain in basic training, and have access to Mind Control soon enough. Refusing to train in these makes solo adventures a lot harder.
And/or a lot more fun and challenging, especially for RP players.
Let's not forget Psychic Scream, which makes the enemy run away for a bit because of the horrific mind/soul pain you inflicted on him. As part of combat, it's a horrific ability. As a way of avoiding combat... well, I suppose once the pain wears off, the victims might be glad you didn't just kill them, but....
And then there's Northrend, home to many an Eldritch Abomination. There are mental debuffs to be found here, such as 'you feel as if something is scratching in your mind' (it doesn't affect your stats, but it's still creepy), and in some areas you will receive whispers from an unclear source, usually urging you toward paranoia.
A very intense version of Mind Rape takes place in Xenosaga Episode 1 where Albedo mentally rapes MOMO in front of the main cast. This is especially powerful given the apparent age of MOMO as a 12 year old girl.
The American version of this scene original Japanese version was modified because the imagery was considered too intense. In the American version Albedo uses lightning-like energy while cradling MOMO's head to extract information, whereas in the Japanese version, he physically sticks his arm into her abdomen. In both instances, the character is shown to exhibit physical as well as mental pain.
Well they clearly did a bad job with cleaning up the American version. Despite never having seen the original Japanese version, I remember being horrified seeing what appeared to be Albedo sticking his arm into MOMO. And thanks to the cut, I wasn't sure if it was her stomach, or something worse.
The nightmare chapters in Max Payne. Max obviously doesn't take well to drugs, as at the end of every part, he's drugged and undergoes a particularly intense night terror which involves the screams of his late wife and child, running across an endless maze, following a trail of blood over a bottomless pit, and confronting himself as the true murderer.
The X-Com games have this as well. The Ethereals and high-ranking Sectoids (and eventually your own soldiers) have two mental attacks: Mind Control and Panic (which lowers morale). Helplessly watching as your own hands slaughter your teammates has to be bad enough, one can only imagine what horrors follow after a heavily-armed soldier is subjected to a Panic attack and goes berserknote they get 255 Turn Units to turn around and fire their weapons randomly until they either run out of Turn Units or ammo.
All of the Boss Banter in American McGee's Alice force her to confront herself. The tougher the Boss, the closer this gets to Mind Rape, with the Jabberwock and the Red Queen remarkably wiping the smirk off her face.
The move Dark Pulse "releases a horrible aura imbued with dark thoughts".
The Pieces of Eden in Assassin's Creed can control human minds this way. In fact, humans were apparently engineered by the Precursors so that they could be controlled via the Pieces.
The BlazBlue series has two variants of psychic Mind Rape, one for Hazama and one for Relius Clover.
Hazama's Ouroboros has this as a built-in function, though he tends to go light on it, preferring to stick to defamatory speeches, Hannibal lectures, and barbed trolling. Pretty much every character subjected to Mind Rape had Hazama as the "therapist", with Noel's regression into Mu-12 as the highlight of his career. At least two characters are shown to be resistant to Hazama - Taokaka, who simply is unable to comprehend his language (so he settles with tearing her to an inch of his life), and Makoto, who served under him in Library Intelligence and is accustomed to his tricks and tactics (which turns out to annoy him greatly when she invariably turns on him).
Relius, on the other hand, decides to skip the trolling and go straight to total decimation, using his research of the soul to filter through your memories, dredging out the worst to break you in record time. If you doubt this is effective, watch Makoto's bad ending - there are no words.
Indie puzzle-platormer The Manipulator allows you to hijack the bodies of guards to either open doors or eliminate other hostiles. Once they have served their purpose you can either peacefully release your control over them - or mind rape them to death. There's no speech, but seeing OH GOD! or IT HURTS! in increasingly larger and distorted text as you kill them is more than a little unnerving.
Implied to happen to 'claptrapped' enemies in Borderlands.
Demonic possession in most cases. During the Fade sequence in Dragon Age II Keeper Marethari comments that most Dreamers are feeble-minded enough that an onslaught of demons destroys their minds.
Interestingly, if Feynriel is spared in "Night Terrors" and not made Tranquil or possessed, he goes to Tevinter to learn how to better control his powers. In a later Act III quest, it is revealed he uses those powers to make a group of would-be gang rapists kill each other while they are still awake.
The Song of the Old Gods and of a few VERY powerful darkspawn, like Corypheus appears to be this. If you play the Dalish Elf origin, you will eventually meet a tainted elf ghoul, your old friend Tamlen, who has been driven mad by it and attacks you, begging you to put him out of his misery. And in the Legacy DLC for Dragon Age II, if you take along Anders (who, as a Grey Warden, bears the darkspawn taint) he will periodically start whimpering in terror about "make it stop talking" and "get out of my head" and will eventually lose control and attack you. 'It' is Corypheus the Emissary.
In the final battle of the first God of War game, Ares does this to Kratos by trapping him in his own mind, taking him back to the night he killed his own family. Kratos valiantly fights off clones of himself while hugging his family to keep them alive...but his efforts are for naught as Ares rips off the Blades of Chaos and kills them. Kratos falls to his knees sobbing as he watches his family die by his blades again.
EVE Online has a particularly harrowing and unpleasant form of this detailed in the "Methods of Torture: Caldari" chronicle - made all the more so by what it doesn't explain. There's an unlabelled box with some electrodes which are attached to the victim, and a circular dial marked only with a line of increasing thickness around its circumference. Questions are asked. When the answers are unsatisfactory, the dial is turned.
It is a symptom of madness that thoughts become uncontrollably disjointed. This can be encouraged.
Shows up in Monkey Island, of all places. The MacGuffin of the fourth game, a mystical artifact known as the Ultimate Insult, works by projecting insults in the primal language (actually monkey noises) that all humans understand on an instinctual level directly into a person's soul until it is utterly destroyed.
The "Dragonrend" Shout in Skyrim essentially Mind Rapes a Dragon by forcing it to experience mortality.
The Dragonborn DLC introduces the Black Books of Hermaeus Mora. Most people who read them (such as a madman you can randomly encounter) go insane; the wizard Neloth says that Herma-Mora occasionally sucks people's minds dry in his bid for their knowledge. This happens to Storn, who willingly lets his knowledge of Skaal tradition be taken by Herma-Mora so that the Dragonborn can complete the Deal with the Devil necessary to kill Miraak.
Mother Maya is a vicious Mind Rape specialist in Shin Megami Tensei: Strange Journey. Her domain, Sector Grus, is a Psychological Torment Zone, and you are often treated to the joyful spectacle of being mind raped or seeing other victims, especially Zelenin and the Ubergestalt (Commander Gore). Also, the Delphinus Parasite is an Energy Being which doubles as a Hate Plague, making it extremely difficult to cure, and which is the broken form of the soul of the resident Monster Lord, Asura. Which is not to say the Law side does not have some good ideas themselves: Zelenin's Song is commented to feel "like nails on a chalkboard" by bystanders not directly targeted, and a heavenly chant by those affected. Said victims were reduced into a tribe of nigh-mindless zealots, barely existing for anything beyond praising "the Lord".
In Shin Megami Tensei IV, the Four Archangels do this to the entire Eastern Kingdom of Mikado through an exceedingly gentle take on this, casually destroying memories and trampling over minds and souls through dreams while presenting themselves as the nice, new rulers of the kingdom, with potent light imagery and much demon destroying to reinforce the people's faith in them. In the Law Path, Mikado ends up completely under Merkabah's thumb, and everyone there is left much more mellow and docile. In the Neutral Path, when you kill Merkabah, the people start waking from this.
The Avatar in Fire Emblem Awakening experiences this when Validar or Grima attempts to take control of them. It's also explained that Validar had also done this to Aversa, implanting her with Fake Memories: he didn't save her life and take her in when she was a very young girl, but murdered her family and then brainwashed her to make her his servant.
To prevent other humans from following the resistance's lead in Shin Super Robot Wars, Char is having the Angel Halo built in Side 2: a giant brain wave amplifier aimed at the Earth. The idea is to amplify Zanscare queen Maria's brain waves and bend the Earthlings to mind control them all... well, to pacify them in any case. Even Laodecia is rather astounded that this feat is possible, and tells Char to go ahead.
Suikoden III has this between twinbrothers Luc (see Jerkass) and Sasarai. It is not enough for Luc to simply hijack the true rune but in the process inform his brother that they are actually clones of Harmonian ruler Hikusaak as vessels for true runes. Sasarai is not amused and becomes physically ill at this knowledge, leading to his Heel-Face Turn once he recovers. His post-game text suggests he did not fully recover.
The True Earth Rune theft scene becomes all the more a mind rape given the mangaka seemed to depict events like an actual rape. This only promotes the significant Twincest fan following for these two.
In Second Sight before the game begins, John Vattic is tortured by NSE director Hanson with a combination of mind-altering drugs, vicious beatings, and horrific images. All the while, Hanson's digitally altered voice echoes through the room, insulting him and blaming him for the deaths that occurred in the playable backstory. Apparently, this torture session was intended to break down John's psyche, forcing him to reveal his psychic abilities to the onlookers, and eventually obliterate his memories. The final and by far the most painful moment of this scene is when Hanson actually enters the interrogation room, and informs John that he's the only friend he has left; John's so traumatised, he can scarcely remember a thing, so he tearfully submits to Hanson's scheme.
Jayne Wilde suffers a similar treatment before being committed to an insane asylum.
In Leliana's Song (a DLC for Dragon Age: Origins), the title character is mentally and almost certainly literally raped by Captain Raleigh,and by the woman who trained her for years and Leliana trusted absolutely. As a prequel to the main game, this basically sets up the events that make Marjolaine so damn good at getting in Leliana's head; even a fair while after her quest (unless you rush her dialogue), Leliana still dwells on the similarities between herself and Marjolaine. If you choose to let Marjolaine go, it haunts Leliana so much that at the end she decides to hunt down her former mentor. See also: Break the Cutie.
When the Messiah is chosen in Duel Savior Destiny they undergo brutal mental and possibly physical agony. It's not actually intentional, though. Rather, they lack the information required to make an informed decision and thus everything they need to know is simply crammed into their head all at once.
The Qunari in Dragon Age do try their best to find proper roles for everyone in the Qun, even their captives. If said captives prove uncooperative, the Qunari break out the "qamek", a poison that drives them insane and reduces them to mindless slaves called Viddath-bas.