In the novel, the actual Mission Control, staffed by sane and non-murderous humans, is still there for Bowman and he finds out exactly what went wrong with Hal and why. This is cold comfort to Bowman, who's over an hour away by radio (the Solar System is a big place, even at light speed) and more alone than anyone has ever been. And in the end, all Mission Control can do is sit there while he utters his Famous Last Words (which oddly enough you don't get to hear him say in the original film - though they are the Cold Open for the sequel).
"My God - it's full of stars!" And it is. Literally.
In Iron Man 3 JARVIS goes a bit loopy after the attack Tony's mansion leaves them stranded in the middle of nowhere in a damaged suit..
Jarvis: Sir, I think I need to sleep now...
Moon Base in Destination: Void by Frank Herbert. The Earthling is the 7th Voidship and all six previous ones have been destroyed on orders from Moon Base. Every crew member has been brainwashed in such a way as to, should the proper orders be given, play their part in the destruction of the ship. And Moon Base gives those orders like crazy. There are multiple redundant switches to blow up the ship. The ship is designed to fail, and directives for recovering from that failure are deliberately suicidal, with almost everyone involved sure they will result in the destruction of the ship. The intent is not to kill them, but to put them in a situation where they have to solve the real problem they were sent to solve—or die.
In Timothy Zahn's Spectre Of The Past, Control directs Luke (in disguise as a pilot) through the pirates' base. Then he taunts him about the Jedi trap he led him into.
World War Z. USAF pilot Christina Eliopolis relates to the interviewer how, after her plane went down in zombie territory, a local "Sky Watcher" going by the handle "Mets Fan" talked her through the hike over land to a rescue point. Only when she's finished telling the story do Christina and the interviewer remark on the fact that her radio was found to have been ruined in the crash, and that no one ever found Mets, the cabin that she claimed to be holed up in, or any evidence that a Sky Watcher using the handle "Mets Fan" ever existed. Her Mission Control was probably a hallucination.
The Plan in N or M is to invoke this; the Nazi agents in Britain will, on a certain day, feed enough false orders to throw Britain into disarray, allowing a Nazi takeover with a minimum of resistance. Fortunately, British counterintelligence has a couple aces up its sleeve, both named Beresford.
In the manhua Infinity Game, D.D. 00, who guides the main party for the beginning of the game is shown to repeat a few sentences twice. This of which is a Foreshadowing on discovering how the Computer Virus was implanted into the game.
This can depend on your GM. Done right, it can liven up the game with paranoia and unpredictability, keeping the players on their toes. Done wrong, and it might just seem more like a Killer Game Master is making with the Rocks Fall, Everyone Dies.
Paranoia. Depending on play style, the role of Mission Control may be filled by The Computer, or by a more traditional Mission Control staffed by clones.
GLaDOS from Portal. At first she appears to be going through technical difficulties. It's arguable whether the trope was downplayed or subverted, though, when it later becomes obvious that she's deliberately screwing with Chel, partly because GLaDOS enjoys doing so, partly because she's crazy since she really doesn't work as intended.
In Portal 2, GLaDOS is back, and is no longer as insanely homicidal as she is vengeful. Wheatley, on the other hand, well, let's just say it's not an accident that he's apparently a complete moron. Cave Johnson also counts, posthumously, to judge by the recorded messages he left behind.
The first-person puzzle-platformer Twin Sector borrows quite a bit from Portal in terms of setting and concept. It should come as no surprise when your A.I. task-giver turns out to be a malevolent maniac.
The voice from Give Up Robot 1 & 2. The voice acts as Mission Control, but either hates your guts or is totally insane. It introduces each game with your "orders," which are garbled and quickly corrected, and congratulates you when you die while telling you to give up or that it hates you if you beat a level.
That said, the computer voice's sole purpose appears to be tormenting Robot — or capturing him when he escapes from their little world in the sequel.
The narrator from Bastion starts to do this when The Kid accidentally inhales some mushroom spores. Most of the lines are repeats of lines from before, but with negative emphasis. The fact he's normally a reliable narrator makes this level extremely creepy. The creepiest part is when he starts humming Zia's song.
It must be noted that the narrator usually only narrates after the player performs actions, though, so he's not really Mission Control.
The narrator/voice/whatever the hell from Loved. The voice presents occasional questions to the player, and then does the opposite of what the answer would logically prompt. When you disobey its commands, it asks, "Why do you hate me?" as though it were expecting otherwise. Example:
Throw yourself into the barbs. Player: "Hell no." *jumps over barbs* How disappointing.
The voice from Depict1 by Kyle Pulver. It professes a desire to protect you and keep you safe while simultaneously giving orders that get your character killed, if followed.
343 Guilty Spark, and later Cortana, in the Halo series.
The Joker in Batman: Arkham Asylum serves as this for the enemy minions. As it becomes clear that they can't actually do anything to stop Batman, the Joker starts taunting them about how Batman is probably right above them.
Any of the AIs in Marathon that aid, or pretend to aid, the player are examples of this. Leela is nice and helpful, but grows less and less coherent as she's being hacked by the enemy. Durandal is completely insane and would rather mess with you, write songs, or ramble about his personal philosophy than actually give you your mission objectives. He gets better in the second game, but he still has his moments. Tycho is outright malevolent and constantly abuses you, and Thoth is an ancient AI who is barely even comprehensible.
Your future (and, later, past) selves in Time Fcuk count as this.
In Metal Gear, Big Boss was Solid Snake's handler for the mission, and partway through, he starts giving you orders that put you in danger, or send you back to the starting area. He even goes so far as to tell you the mission is over, and that you need to turn your console off. Of course, it turns out Big Boss is behind everything, and he fully expected you to get killed before you got as far as you did, so he started actively trying to get you killed.
Master Miller in Metal Gear Solid, who is actually Liquid Snake in disguise, sabotaging the mission by making the Colonel suspicious of Naomi, and cluing Snake in on the true nature of his mission and the FoxDie virus. Neither Campbell nor Snake notice until Liquid breaks his kayfabe, and Campbell notices that Miller's transmissions have been coming from Shadow Moses all along.
The Colonel in Metal Gear Solid 2 towards the end starts to break the fourth wall even more than the series usually does, and talks about things like aliens, gardening safety, and the fact that he needs scissors. 61. He turns out to be an AI impersonating the real Colonel from Metal Gear Solid; and the nonsense ocurrs thanks to a computer virus that corrupts the AI.
The off-his-meds Colonel even made it into Super Smash Bros. Brawl, appearing when Snake uses his Smash taunt against Luigi. While the AI isn't as nonsensical as before, you can still tell it's the AI when he gets to the "La Li Lu Le Lo" part.
Xana of Dark Messiah is fused to the player and functions like a typical mission control. As you get farther in the game, her comments become more and more blatantly evil and eventually on the insane side. Of course, it's not secret from the very start that Xana isn't nice or all there.
Red from Penumbra: Overture is a nice-ish guy and his advice is usually pretty good if you can separate it from everything else he says, but from the first moment he talks to you, it's clear that he's not, strictly speaking, all there. He does try to kill you once or twice as revenge for insulting him with your judging, judging silence, but doesn't see why that should stand in the way of the pair of you being the bestest pals.
How does my brain-flesh know your fluids are leaking? Because Red tricked you! (laughter) Spidery tunnel was far from a necessary evil, more-so it served more as a well deserved punishment. You thought my mind had been lost to the ravages of time, but poetic justice has struck with a sonnet and an eight legged baptism of fire! With justice now served cold, I hope we can be good friends.
The sequel Black Plague features Clarence, a voice in your head who spends half his time trying to get you killed, the other half trying to keep you alive, and every moment he can insulting you, rifling through your memories, screwing with your perceptions and generally being a huge jerk.
Jodie from Metal Wolf Chaos may be unambiguously on the player's side, but also happens to be completely insane.
The Tower's God in Tower Of Heaven starts out as a slightly arrogant, but more or less just divinity who wants to test your abilities to see if you are worthy of being rewarded. As you progress, he becomes increasingly hostile and intent on making you fail, as he imposes more and more random and unjust rules on you. By the tenth level, he experiences a true Villainous Breakdown:
"How... How dare you continue to live?! Is it merely to spite me? You damn fool!"
In 1213, it is increasingly difficult to tell if Westbury is trying to kill you or help you escape, but he is definitely not at all there. The commentary explicitly points out that Westbury's mind has been completely snapped by the circumstances that led to everyone being trapped on the space station, and doesn't care what he has to do to get off it.
The voice that guides the protagonist of K.O.L.M. belongs to his emotionally abusive mother, who claims to have a plan for him but refuses to explain it. Once he gets the item she needs, she tries to get him killed.
In Command & Conquer: Renegade, the automated anouncer in the Temple of Nod goes completely nuts after the Temple is hit with an ion cannon strike, randomly blurting out non-sequiturs like "Intruder alert! Alert cancelled! Intruder alert! Alert cancelled! Intruder alert! Intruder cancelled! All intruders please report to the detention centre for debriefing!"
In Jables's Adventure, Squiddy is something of a Cloudcuckoolander. He tries to teach you how to break blocks with your mind (you can't), and every time you collect a fruit he tells you a fact about the fruit that may or may not be complete nonsense (some of which even he doesn't believe).
While Fallout: New Vegas might not have any good examples in the game proper, the Dead Money addon gives us Father Elijah, the man who abducted you and mastermind of the Sierra Madre heist. He gives you general orders which, frankly, would be tantamount to suicide if anyone but the Courier were assigned them. He specifically states that once You Have Outlived Your Usefulness, he'll detonate your bomb collar so you don't get in the way.
Likewise for Professor Calvert] in the Fallout 3 DLC Point Lookout, who activates a squad of robots to kill you after outliving your usefulness.
The Mentats-addicted Think Tank members in Old World Blues use the Courier to retrieve the three Old World technologies so they can escape the crater and conduct their experiments on the citizens of the Mojave. Unlike the above examples, you can reason with them rather than killing them.
The Mission Control named Mission Control from Thelemite is explicitly sending you on suicide missions because the organization it works for didn't allocate enough of the budget to incinerate the mutant player character after the experiment that created him. Eventually, he just gives up on that and tries to kill you directly as the final boss.
The Announcer in Team Fortress 2 clearly has a bit of a personality problem and is in charge of both teams, but before they fixed that glitch, when a King of the Hill game went into overtimenote "Overtime! Overtime! Overtime! Overtime! Overtime! Overtime! Overtime! Overtime! Overtime! Overtime! Overtime! Overtime!", she clearly went off her meds. Even with the fix she pretty well loses it whenever the cart has almost reached the final terminus.
An argument could be made for Adam Malkovich along these lines. His timing in authorizing the use of each piece of equipment could be likened to telling a drowning man about this great new invention called a lifejacket. Insane if not malicious, and incompetent if not insane.
The Guardian in Ultima VII. He goes out of his way to be helpful for a little while at first, but rapidly moves on to trying to get you killed.
Dungeon Keeper has a mission control who's helpful through most of the game, but in the last level apparently lets your successes go to his head, and counsels you to destroy the enemy base so you can reclaim the Avatar. This is an absolutely terrible idea, as the enemy base cannot be claimed due to your inability to build bridges, which greatly inhibits your ability to reinforce or regroup your troops. Which you'll want to do, because their base is also stuffed full of traps, doors, high level vampires that use their wind spell to scatter your forces all over while using their Drain, Heal, and ability to repeatedly resurrect to be incredibly difficult to take out, while the enemy keeper will disease your troops and start pounding them with lightning. Alternatively you could ignore him, sneak up a side passage, and reach the Avatar without the enemy doing a thing to stop you.
Towards the end of Iji, barring an Easter Egg, Dan gets killed. Iji drags his body to a bed, convinces herself that he's still alive, and starts responding to imaginary prompts as if he were still giving them.
Variation in Eternal Darkness - The closest thing Alex Roivas has to Mission Control is her grandfather's ghost, who occasionally offers supportive words and advice betwen chapters. Late in the game he starts sounding more sinister, eventually telling Alex that he hated having to raise her after her parents died. Of course, that was just the Liche messing with her, and she saw through the illusion.
In The Incredible Hulk: Ultimate Destruction, Samson acts as Hulk's mission control, giving him objectives via simple, one-word hypnotic suggestions in his mind ("Destroy", "Retrieve", "Protect", etc."). However, during one mission he sends Hulk off to destroy several military buildings, gleefully whispering, "Do it, Hulk. Blow them to smithereens..." It turns out it's actually Devil Hulk, a malevolent new personality emerging from Bruce's psyche and tricking him into attacking civilians.
In Spec Ops: The Line, you don't have a Mission Control. You do, however, have little Objective checkboxes in the upper left of your screen. Late in the game, they start getting... odd, giving you objectives such as "Obey" or "Run, goddammit!". The enemies get a straight example in the Radioman, who gets his kicks by mocking the men he's sending to their deaths.
In Far Cry 3, Buck sends Jason to find a Chinese dagger. The whole while, he sends him on ridiculously dangerous tasks that are nearly suicidal, acts condescending and treats Jason like a disobedient schoolboy. Later, this trope is given a twist. You find out that the helpful Rakyat, who empowered you with the tatau and help teach you to survive and rescue your friends, have been doing so ultimately to have you become their greatest warrior, and try to make you kill those same friends.
Tasselfoot in Give Up (no relation to Give Up Robot) stops being helpful after the second stage, and begins trying to persuade you to hit the "GIVE UP" button at the bottom of the screen. He becomes increasingly insulting and spiteful with each level you complete.
In the invasion of Panama in Call of Duty: Black Ops 2, Hudson deliberately misleads Mason and Woods for the entire mission, which is usually blamed on faulty comms. It ultimately leads to Mason dying... or maybe not.
PlanetSide 2 is full of raging General Failures yelling conflicting orders - as becoming a Commander (ability to give server-wide orders and attack/defense requests) simply requires a few unlocks. It's not uncommon for one commander to call an attack on a Tech Station, then for another to call for the defense of a Biolab, causing both to start yelling at each other over the global orders channel. Other times, the Orders chat is used to give completely inane advice (Remember to brush your teeth before bed!) or yell propaganda (PRAISE MALORN! BUFF THECARV!)
First-person horror game Daylight begins In Media Res, although it becomes pretty clear rather quickly that there's something sinister and not-quite-right about the mysterious voice on the radio giving you orders.
Castle Heterodyne in Girl Genius acts like this to the team of prisoners attempting to repair it. While it's homicidal at the best of times, the problem is intensified by the castle's damage causing a fracturing of its personality. Fragment A might kill all repair crews entering an area that Fragment B desperately wanted repaired, for instance. However, even once Agatha fully restores it, it still hugely abuses its repair crews For the Evulz.
"Oh, come now, we had fun! And alerting you to every other trap was more than fair!"
In Homestuck, many characters do this. Prime offenders are Doc Scratch, Terezi, and Vriska. Kernelsprites merit special mention because although they have access to a great deal of important information about Sburb, they are required to present it one or two pieces at a time, in a roundabout way.
Also, the exiles, especially the ones who don't really know what the consoles do. But with few exceptions, none of them are actively malicious, just kind of adorably incompetent.
Dirk Strider's autoresponder has a few things to answer for itself. It's an AI programmed by Dirk at age 13 to be a perfect copy of his personality at that time, and has developed in its own fashion since then. It seems relatively benign of intent but it still has its own agenda, and is pretty cagey about disclosing what that agenda is.
Vic from Red vs. Blue serves as the liaison to both Red and Blue Command, although the Blood Gulch soldiers don't know that. His advice to both teams generally ranges from irrelevant through obvious to actively harmful.
Tails even starts talking to the audience of the Let's Play, in case you haven't felt the need to start taking antipsychotics yourself.
In the Interactive fiction game You Find Yourself In A Room, the A.I. ABOMI is both insane and completely sadistic. It repeatedly proclaims how it's non-humanity makes it superior to you, throws some brutal, heartbreaking insults your way, and eventually CUTS OFF YOUR HANDS WITH A ROTARY SAW.
Welcome to Night Vale sometimes gives orders or advice to the listener, in "ads", proverbs, or on the twitter. It's usually either creepy or just completely nonsensical.
Hereís a health tip from the Greater Night Vale Medical Community. Itís possible you wonít be able to kill it. If it manages to burrow under your skin, stop fighting, because it has already become part of you. Welcome your new body-mate! Listen to what it has to say, and see where the new symbiotic lifestyle takes you.
In the the World of Warcraft / Silent Hill / Interactive Fiction megapost You Awaken In Razor Hill, the player periodically finds himself with new quests in his log that he doesn't remember picking up. The mysterious quest-giver starts out encouraging and helpful, makes a gradual slide into the creepy and over-familiar, and eventually veers over into full-on homicidal sadism (and in fact eventually turns out to be the Eldritch Abomination responsible for this world in the first place.)
In the Kim Possible episode "Hidden Talents", Wade directs Kim and Ron to grab one of Professor Dementor's inventions, deliver it to a drop-off point, and leave without seeing the recipient. Kim finds this odd, but takes his word for it and carries out the mission. "Wade" is actually Dr. Drakken, hacking into the Kimmunicator line and using CGI to impersonate Wade.
Teletraan One in The Transformers episode Kremzeek, after the title character damages him.
"Alert! Alert! Evil Martian flangoes have invaded supermarkets across the planet. They have come to steal Earth's ammonia." "Choco rations down 2 grams! Doubleplusungood!"