Himeno Awayuki of Prétear was told that she "doesn't need to know" the backstory, but forced the Leafe Knights to reveal it anyway — specifically, that their enemy is the previous Pretear, who turned evil because of her unrequited love for Hayate, and that Himeno herself may end up turning evil as well. Cue Heroic BSOD. In the anime version, the consequences were even worse.
The heroine of Kamikaze Kaitou Jeanne is a Magical Girl on a mission from God. About halfway through the series (or towards the end, in the anime), she finds out that she's been working for Satan all along, her Mentor Mascot is a fallen angel who was in on the whole thing, and the two have been conspiring to break her — in Satan's case, he's been doing it since she was an infant.
In the manga version of Chrono Crusade, part of what inspires Aion's Evil Plan is the Awful Truth he found out about his origins (that is, that the demons are really aliens, and the current Hive Queen was a human woman pregnant with twins (Chrono and Aion) before she was turned into a demon). He also goes to great lengths to hide the truth from Chrono, saying he "doesn't need to know"—but Chrono finds out in the end and takes it rather well, actually.
In Detective Conan, Ai keeps insisting to Conan that if Ran were to know the truth about the Black Organization and Shinichi being Conan, then she will not smile. She will be burdened by the truth.
Sasuke was far happier thinking his brother just went around killing family members because he was bored than when he found out that he had really been acting under orders from Konoha. He was a lot saner then, too.
Anyone who wants to become a Magical Girl in Puella Magi Madoka Magica must know one thing: upon making the contract to become a magical girl, your soul gets sucked into the Soul Gem that you use to transform into your magical girl form, and if it's not within 100 meters of you, your body becomes an Empty Shell. This essentially turns you into a Lich.
Two things, as of Episode 8. The warning that Kyubey gave the girls about needing to keep their Soul Gems clean by charging them with Grief Seeds? If they don't regularly purify the corrupted gem and it darkens completely, it becomes a Grief Seed and then explodes, transforming them into a Witch. Just in case that wasn't horrifying enough, this is apparently inevitable. Ultimately the gem will darken completely no matter what the girls do, and every magical girl is doomed to become one of the Eldritch Abominations that she and others like her fight. And the only way to avoid this horrible fate? Die before it can happen.
And just to make things even worse? Apart from witches created from former familiars that grew their own Grief Seeds after their parent witch was killed, every single witch that the magical girls have fought was once a magical girl herself. Every magical girl became a magical girl through making a contract with Kyubey. This means that Kyubey creates witches, meaning that all the bad things that witches do to people and all the horrible things that magical girls have to go through to stop them are ultimately Kyubey's fault. There's a REASON that a lot of people despise the little fucker.
To top it all off, the reasonKyubey is doing all of this? The entire universe is dying.
The second episode (and the latter part of the first) of Shakugan no Shana, Shana explains that people get eaten from existence, between the space of seconds, and it is such a regular occurrence that replacement humans are needed to keep the universe from destabilizing.
Tengen Toppa Gurren Lagann: Continued use of Spiral Power will eventually lead to an event called the Spiral Nemesis, which will give birth to a super-galaxy that will rip the universe apart.
In The Secret Agreement, Kyuusai reveals to Yuuichi that he is from a powerful clan that steals other people's life force, and that neither he nor his boyfriend actually love each other, it's just an implanted delusion between predator and prey that makes it easier for Yuuichi to steal Iori's life. Yuuichi is horrified.
In Madlax, the fact that a very young Margaret had to kill her Brainwashed and Crazy father Richard when he tried to kill her after a plane crash is a truth so awful... that she created two alternate personalities (Madlax herself and Laetitia) to escape it. And she doesn't admit it to herself until the penultimate episode of the anime.
Tripeace: In the chapter with this title we learn that not only did peace-loving Idiot Hero Nana flee from Ares (or possibly Hades) — a group that deliberately incites conflicts because "conflicts will always exist" vs the anti-war TriPeace organization's goal of ending all conflicts forever — he's their founder.
In Neon Genesis Evangelion, Naoko Akagi snapped when a Rei clone taunted her by saying Gendo never loved her and frequently called her an old hag. And by snapped, I mean she strangled the little girl to death right then and there. Her daughter Ritsuko eventually had a similar breakdown, including the murder, when she realized Gendo felt the same way about her too.
That's not even CLOSE to the worst Awful Truth in this series. SEELE wants to end the world. The Evas hold the souls of the pilots' mothers (who almost always died unpleasant deaths). Rei's only purpose is to be a disposable sacrifice for SEELE's Assimilation Plot. The hits just keep coming.
In Saki Achiga-Hen, Kirame overhears a conversation between her school's mahjong club president and her best friend that she wasn't chosen to be on the team for her skill, but because she never falls below 0 points, enabling her to stay in the game no matter how strong the vanguard player is, while her teammates recover the points in the following rounds. She doesn't get upset, but is instead happy that someone has a use for her talent.
In the main series, Saki's primary goal is to reconnect with her sister; due to an only vaguely glimpsed at event that was most likely related to their parents separating, Teru is refusing to speak with Saki. Saki is quite disturbed to hear, third-hand, that Teru is denying that she has a sister. While Saki expected Teru to say something like that, she wonders if they can ever possibly reconcile.
In Girls und Panzer, during the prequel manga, Little Army, Miho learns that her sister Maho, whom she looked up to, won the tournament by firing on the enemy flag tank when it was going to rescue one of her team's tanks. This causes a temporary rift between Miho and Maho when Maho begins acting coldly around Miho around the time of their mother's return, when she's confronted about this, but while their relationship is mended, it causes Miho to realize just what the Nishizumi style expects of those who pursue it, and thus causes her to seek out her own way of tankery.
In Berserk, the Awful Truth of the Berserk setting isn't that God Is Evil. Nor is it You Can't Fight Fate. The Awful Truth is that humanity wouldn't have it any other way. They need an evil "god" to dictate their lives because the alternative is worse: that their suffering is meaningless and they have no one to blame for it but themselves. They needed it so badly that they subconsciously willed it into existence.
The conclusion of Watchmen: Ozymandias schemed a gigantic plot to have a fake 'alien' kill millions in New York in order to unite humanity against a perceived common enemy and stop nuclear escalation. And after all that, it may only have worked temporarily.
Enigma features a villain called The Truth who has the power to look someone in the eye and strip away every single comforting lie they tell themselves. Most of them either commit suicide immediately after, or else go on a killing spree.
Destiny is a Hazy Thing: Kushina learns (from Naruto) that Minato put in a brainwashing function in Naruto's seal that would've turned him into the optimistic (Idiot Hero) messiah we see in canon had the seal not been messed with. Doubly tragic because Kushina thought Naruto was lied to and sided with Minato.
Adventure Time fanfic has it with Alex: she's the reason Marceline and Princess Bubblegum hate each other as she started their falling out.
The Awful Truth Elly Patterson kept from her family because she feared ostracism in The New Retcons is she has an illegitimate daughter she gave up for adoption. Elizabeth and April took it rather well. Michael and John did not.
Michael had an additional Awful Truth he didn't take well. John isn't his biological father.
And then Anthony has one. His father killed his mother. He managed to rationalize it though by realizing that it was probably Accidental Murder, since his MO would be to wait until she cheated and stiff her on alimony and child support.
Naruto:Asunder; Minato and Kushina are still alive and expect Naruto to be happy about it. They find out he wants nothing to do with them and that their excuses to justify turning him into a jinchuuriki aren't gonna cut it.
Naruto: "THAT'S THE PROBLEM! YOU DIDN'T THINK! Too busy caught up in your FANTASIES chasing after a teme who doesn't barely give you the time of day, to stop to consider how OTHER PEOPLE will feel when you decide to find some way of IMPRESSING that teme! I'm glad you never went on a date with me! Now I realize that you never were the type of girl I'd have wanted to have a relationship with!"
Crosses with Family-Unfriendly Aesop in Team 8 where Kurenai tells Naruto that no matter what he does and even if he becomes Hokage, there will still be people in the village who will hate him because of the Kyuubi.
The awful truth Papa Smurf was trying to keep from Empath until his 150th birthday in Empath: The Luckiest Smurf? Empath is Papa Smurf's only biological son, and Papa Smurf had purposely sent Empath away to Psychelia because he feared how his son would be treated by his fellow Smurfs because of his telepathic and telekinetic powers.
In the Korean movie Old Boy, Dae-su is kidnapped, imprisoned for 15 years, and then released with no explanation. After finding and confronting the man responsible, Dae-su finds out the Awful Truth isn't "Why he was imprisoned" but "Why he was released." He goes mad from the revelation and cuts his own tongue off with scissors.
ParaNorman: After an hour of being essentially an action-comedy, it is revealed that the Witch is actually a young girl named Agatha Prenderghast, who was wrongfully executed by the townsfolk 300 years ago, after which the movie takes on a significantly more somber and melancholic tone.
A major motif in this series is the fact that there are some things that you just can't unlearn. The kids can't, although they desperately want to, forget about the Yeerks and go on living their lives, because they now know they'd be dooming the entire planet to enslavement; to quote a Megamorphs back cover, "You can't close your eyes to the truth you know is out there".
Subverted in one instance, when Jake strikes a deal with Crayak to return them to the moment where they chose not to walk through the construction site (where they met Elfangor and learned of the invasion). The kids walked home the safe way and consequently they had no knowledge of the Yeerks or the invasion. But, true to the theme of the series, the kids eventually have to confront the reality they didn't even know was there (made even cooler because now they don't have any powers).
Harry Potter: In Harry Potter and the Philosopher's Stone, when Harry asks Dumbledore why Voldemort wanted to kill him in the first place, Dumbledore's response is more or less that Harry is not yet ready to hear the Awful Truth, but at least makes clear that he has the intentions to tell him some day. Intentions being the key word here, as Dumbledore puts this off until the fifth book and only tells Harry then because Dumbledore's keeping the truth from Harry backfired rather badly, leading to Sirius's death. Dumbledore, to his credit, does at least acknowledge that this was pretty dumb. This isn't the only instance, but probably the most significant as much of the plot revolves around adults trying to protect Harry from the awful truth.
This also plays a rather large role in the third book. First with Cornelius Fudge's insistence that no one tell Harry that Sirius Black is out to get them because it might scare him. Proving that not all adults are complete idiots, Mr. Weasley planned on telling Harry anyway, telling Harry to be careful and warns him not to go looking for Black. But he also falls into this trope by refusing to answer when Harry asks why would he be stupid enough to looking for someone who wants to kill him. Harry finds out anyway, but proves Mr. Weasley's fears correct because the Awful Truth in fact makes him want to kill Black. However, in this case, the Awful Truth isn't even the Truth at all because Peter Pettigrew, not Sirius Black is responsible for his parents deaths and Sirius escaped Azkaban to kill Peter Pettigrew, not Harry.
This was all necessary for Dumbledore's plan to work. In the first place, he wasn't even sure that Harry would survive, though he had guessed Harry might due to events in Harry Potter and the Goblet of Fire, and as he himself has said, his guesses are usually right. But even if he had hard evidence that Harry would be able to survive, he couldn't have told him, because if Harry didn't think he was going to die, how could he sacrifice himself for everyone in the castle? So in this case, it was more revealing the Awful Truth while hiding the Wonderful Truth that accompanied it.
The Prayer Of Miriam Cohen by Rudyard Kipling unfolds this trope. Not in very flattering way, though.
In Catherine Asaro's The Misted CliffsBack Story, Dancer left her husband with her son to return to her abusive father, who battered both her and her son, Cobalt. When he was grown, Cobalt rescued his father and found him to be a loving and affectionate man, but his mother refuses to explain. At the end of the book, Dancer explains to her son's wife, Mel, that there is reason to think that her son is not her husband's but his half-brother's child, and under the law, they would have executed her and her lover and her son. And they can not tell Cobalt because it would break him.
In the sequel The Dawn Star, his dying grandfather tells Cobalt a secret. Throughout the book, Mel is terrified that the grandfather guessed and told him. At the end, Cobalt reveals that he had said that Dancer was not, in fact, his daughter.
In The Gunslinger, the first novel of The Dark Tower, when the Walter makes the town drunk return from the dead, Walter says "If you tell him the number 19, he will tell you what lies beyond death." When one woman does this, despite Roland's urging, she Goes Mad From The Revelation and begs Roland to kill her.
Sort of inverted in Silverfall: mentor desperately wishes her [in]subordinate could understand.
Qilue: If you doubt me, curl yourself around the Ladystone to sleep tonight, pray to Eilistraee for judgment upon me, and learn your answer. [...] Yes, do that. [...] Learn the truth. Thalaera: Will I be maimed? Qilue: Hurt, perhaps; maimed, no. Thalaera: Hurt? Qilue: Truths have sharp edges. Learning the truth often hurts.
Galaxy of Fear has the revelation about Hoole, who for the first several books has some secret which his niece and nephew only get to see the edges of. When Tash and Zak find out what he was hiding, they rage at and abandon him, though they come back later.
In the Incarnations of Immortality novel "For the Love of Evil," the demon Lilith (yes, That Lilith) does a magnificent job corrupting Parry through lust and uses these to destroy his ego, such as "You will do what we need, solely because of your animal lust. And you will rue this one decision the rest of your days."
In Oedipus Rex the title character is warned by the soothsayer Tiresias that he really doesn't want to know the truth, but tragic pride gives Oedipus the persistence to find out.
In The Dresden Files, this is played in several different ways. First, anytime Harry has to let people in on the masquerade, he tells them straight up that they're probably never going to sleep well again. Also, when Harry confronts his mentor, Ebenezer, and Ebenezer tells Harry that he's the Blackstaff.
Used with Murphy, as that's what led to his realization that some times people need to be told the truth. For the first three books, she's wary of him because he's so ambiguous all the time and nearly gets herself killed on a number of occasions— and she's always almost-arresting Harry. He finally explains everything to her in Summer Knight, which leads to a much closer friendship and a couple levels of badass on Murphy's part.
'There is not enough room in your head to understand what I could tell you. I have seen the forces that really hold this universe together, and it isn't your Emperor. All you Imperial vermin devote your lives to crushing the spirits of mankind until not one man or woman could survive knowing the truth.'
The Grey Knights themselves are an example. Any average Imperial citizen who learns of their existence is killed out of hand. Even Space Marines who learn about the Knights without authorization are mind-scrubbed to remove the truth.
In the Vorkosigan Saga novel The Warrior's Apprentice, Elena searches for her long lost mother. She finally learns her mother's identity when said mother takes bloody revenge on Elena's father for repeatedly raping her when she was a prisoner of war. Likewise, the main plot of The Vor Game is triggered by Gregor learning that his late father was a rapist and murderer.
In the Ender’s Game book Shadow of the Hegemon, Bean learns from a posthumous letter the Awful Truth about his own birth: That his increased intellect has a side effect in that he will never ever stop growing, and will ultimately die young of the Square/Cube Law because either his heart will not be able to maintain a body his size or his huge body will crush his spine.
Speaking of Ender’s Game, the fact that Ender was not playing a game but committing genocide is a prime example.
In the Spellsinger spinoff, Son of Spellsinger, the Grand Veritable is a magical, sentient lie detector that can not stop declaring the truth. Fun ensues as it wrecks relationships across the Bellwoods.
In Ursula K. Le Guin's short story "The Ones Who Walk Away from Omelas", a child is brutally tortured to maintain the prosperity of the eponymous city. At some point in their lives every citizen of Omelas sees the child and learns of the connection between the child's suffering and the city's well being. The title refers to the people who can't live with the Awful Truth anymore and leave Omelas forever.
Even aside from the substantial amount of philosophical musings on this trope (where it is nearly referenced by name), Sergey Lukyanenko's Night Watch has more than its fair share of examples. Early on, for instance, the protagonist Anton runs into a seemingly random cursed woman on the metro who he tries to help out. Soon, the events at the beginning of the plot which seemed to be important are discarded to focus on her. In the end, however, it turns out that everything that happened was part of a plot to recruit the woman, who turns out to be a future Great Sorceress, that is a magician of immense power, into the Night Watch. Including the (twice!) attempted murder of a child, and the possible deaths of every member of the Night Watch in Moscow.
In the dénouement of Aunt Dimity Takes a Holiday, Derek's cousin Simon and his father father finally tell him that his mother died of cancer, and that she wanted it kept from him (Derek was seven at the time) because the disease and its treatment had a drastic effect on her appearance. The Earl says: "She lost her hair, her fingernails, her teeth. Her skin turned gray, her body shriveled. You were her darling child, the only one she would ever have.. She didn't want you to remember her that way. She wouldn't let me tell you...." Derek grew up believing his father had alienated his mother ("My mother spent the last year of her life in London because my father was a heartless swine. I vowed then and there that I would never be like him."). He took the dismissal of his beloved nanny who showed signs of insanity and was having an affair with the Earl's valet as further evidence of his father's cruel nature, and he changed his name and avoided his father for twenty years.
Battlestar Galactica plays this straight when Kara attempts to figure out how she came back from the dead and when, in the Season 3 finale, Colonel Tigh keeps trying to figure out what the Terrible Ticking is all about. Turns out, they did not want to know. They got better. Averted when Kara finally discovers the meaning of the prophecy that she will "lead them all to their end."
Dexter is essentially a Thirty Awful Truth Pileup, both for the eponymous character and those close to him. In Season 1 he discovers that the reason he is being singled out by the Ice Truck Killer is that the two are brothers. Which wouldn't be terrible in and of itself, but it comes with the realization that Harry Morgan didn't quite tell the whole truth and nothing but the truth: Dexter watched his mother die. Also, Harry's a liar. The Big Bads of Seasons 2 and 3 get awful truth reveals, usually coinciding with their crossing of the Moral Event Horizon. In Season 4, Debra finally finds out the truth about Harry.
Ashes to Ashes: The big reveal(s) at the end of the programme could qualify as The Awful Truth to the character(s) it applies to.
King Uther's refusal to tell Arthur the truth about his magical birth and the death of his mother(s) in Merlin. Arthur seemed to find out in the episode "Sins of the Father", but came to believe Merlin's statement that Morgause lied to him completely instead of only partially.
Morgana revealing herself as the traitor in season 3 is such an Awful Truth that Uther never fully recovers.
The eponymous event in The Event is apparently a truth so awful that the CIA director didn't want to tell the president, much less the viewers.
Director Sterling: "Information about this has always been on a 'need to know' basis."
President Martinez: "I'm the president. I need to know!"
This is a major plot point of The X-Files. The tagline for the show is "the truth is out there", and Mulder spends nearly a decade trying to uncover it. When he does, he finds out why it's been kept hidden from society for sixty years. He was reluctant to even tell Scully, as the Truth is aliens are invading the world in 2012 to colonize it, and there is nothing that can be done to stop it.
Subverted earlier with the truth about his sister, Samantha. The quest to find his sister was the reason Mulder got started on the X-Files, and a when not trying to find out The Truth, he is trying to find out what happened to her. After an extremely confusing plotline, we find out Samantha died in her early teens after years of medical experimentation. It is classified as an awful truth, but Mulder is simply satisfied to finally know what happened to her. The episode is aptly named "Closure", and when Scully asks him at the end of the episode how he is dealing with it, he replies "I'm free."
In the Doctor Who episode "The Beast Below" all subjects of Starship UK are required to "vote" when they turn 16 and every five years thereafter. The are taken to a room where they're shown a video then allowed to either protest, or forget that their civilization is Powered by a Forsaken Child. Everyone seems to choose the mind wipe, and the few that do protest are fed to the star whale.
Terui Ryu finds out that the person who gave him the gear needed for him to be Kamen Rider Accel also gave the Weather Memory to Isaka, the man who killed his family. Then he finds out why she did that.
The Japanese drama Mendol Ikemen has an outright weird one. The manager who has presumably until episode 11 been a lesbian is actually a guy.
Londo Mollari believes that his lover was poisoned by Lord Refa. Mr. Morden arranged Adira's murder to drive Londo back into the Shadows' employ
G'Kar believes that the Security Council was practicing Head-in-the-Sand Management when they refused to believe his claims that the Shadows had returned. He was actually the last to know, and they all had their own reasons to feign ignorance. His homeworld was conquered because nobody would help fight off the Shadow-backed Centauri invasion.
The finale to Season 5 is a definite example of this: Dean learns that the "Upper Management" of Heaven has no intention of stopping Lucifer's return. In fact, they want the Apocalypse to happen so that they can finally destroy Lucifer once and for all (which will also lead to the deaths of billions of innocent people who get caught in the crossfire).
The music video for the song "Just" by Radiohead. A man lies down in the middle of the street, refusing to get up or tell anyone why, because if they knew, they would do the same.
The fact that the New World of Darkness is, well, a World of Darkness is a secret desperately kept from ordinary humans in the eponymous setting. It's an odd example, though, because the books state that a large part of why all the separate Masquerades are in place is for self-preservation: if all of humanity knew the truth, humanity would fight and the supernaturals would lose. The Hunters cause enough problems as it is.
BattleTech: As the Inner Sphere is getting mauled by the technologically superior Clans some believe that the descendants of General Kerensky's Star League Defense Forces (who fled into unknown space centuries ago to avoid getting caught in a civil war and being forced to fight those they swore to protect) will come back to assist them in their darkest hour. A certain mercenary leader... refutes this theory.
Jaime Wolf: "Don't you see? Kerensky's people have returned. They are the Clans.
Warhammer 40,000. Hoo boy... let's just say that the Imperium has a good reason for its proverb "Ignorance is a virtue."
Chaos is the prime example of the Awful Truth. The Inquisition is quite willing to sterilize and relocate anyone who might have learned about it to forced labor camps for the rest of their lives. If this isn't practical, the Inquisition will just kill everyone. This policy can be applied to entire worlds with billions of people on them, and is still considered the humane solution compared to what might happen otherwise.
Experienced Shell-Shocked Senior Auron from Final Fantasy X intentionally keeps the truth regarding the summoners' journey for the Final Aeon, that it is an ultimately futile effort causing much unneeded sacrifice, from the the rest of the characters. When they finally figure it out on their own and demand an explanation from Auron about this, he simply responds, "Would that have stopped you?''
The less-obvious reasoning behind this masquerade is that Auron simply saying "Hey, killing Sin the traditional way just perpetuates the circle of violence" wouldn't be enough to change anything, and would more likely result in the party accepting the situation. By only revealing certain key bits of information as the journey continued, Auron was able to direct them on the path he tried to take before: the rejection of tradition and an attempt at a new world. Almost Magnificent Bastard levels, when you think about it.
He actually outright states that Jecht turned into Sin very early on but it doesn't take because he doesn't explain the story behind it.
Before this, the entire rest the party takes quite a long time to reveal to Tidus that Yuna's journey as a summoner is intended to end with her death summoning the Final Aeon. Understandably, Tidus doesn't take it well.
Wakka: We weren't hiding it!
Lulu: It was just... too hard to say.
Tidus in turn doesn't reveal the Awful Truth he learned at the Fayth Cluster to the rest of the party until right before the final battle: that defeating their opponent Yu Yevon will make Tidus disappear, since Tidus is part of Yu Yevon's Summoning of Dream Zanarkand, and killing Yu Yevon will end the Summoning.
Kevin programmed the original KOS-MOS to kill him so he could become the Red Testament. He died in Shion's arms and she was haunted by the memory for years.
The fit of agony and rage Shion felt upon her parents' deaths is what summoned the Gnosis into the universe in the first place. Febronia knew this but spent the better part of 3 games slowly guiding her to where she could retrieve this repressed trauma.
From the previous page quote, Alex Mercer spends the majority of the game Prototype trying to figure out who was responsible for the viral outbreak which destroyed his memory. The culprit is Doctor Alex Mercer; Mad Scientist. The player character is really just the mass of viral bio-matter that consumed Alex Mercer and assimilated his identity.
Alex Mercer: I looked for the truth. Found it. Didn't like it. Wish to hell I could forget it.
In inFAMOUS, Cole gradually grows to hate the Big Bad, Kessler, as Kessler is both responsible for the event that gave Cole superpowers at the cost of thousands of innocent lives, and eventually kills Cole's girlfriend, all the while spouting rhetoric about how Cole needs to learn what an awful place the world really is instead of pretending it's any better, never offering even a cursory explanation for why he's doing any of it. In the end, just before Kessler dies from wounds Cole inflicts, Kessler reveals via telepathy that he's Cole himself from a Bad Future that exists because he refused to do anything about it when he had the chance, come back in time to traumatize himself so that he'll be prepared to make better choices when those hard decisions come.
Metal Gear Solid 4 pulls a complicated Awful Truth on the protagonist. Solid Snake has started to show indications of accelerated aging; by the time the game starts, he's going on his early 40's, and looks older than his parents (who should be over 80 by then). Otacon explains that it seems like a classic case of Werner's Syndrome, except the tests for the condition say that Snake doesn't have it. They speculate that it's because Snake isn't "normal," meaning that there must have been some fluke in the cloning process that created him, possibly exacerbated by the nanomachine-based artificial virus he was injected with to assassinate certain people by coming into contact with them. In fact, his brother Liquid even suggested as much, saying that the problem arises from the genetic sample that created them being taken when Big Boss was old himself, in his 50s. When Snake finally finds someone who can figure out what's going on, the truth is much worse than any of the speculation: the premature aging is natural, it's an intentional alteration made during the cloning process to give him an expiration date, which means there is no way to fix it and he will die of old age within six months, probably before turning 42. Worse, the nano-virus in his blood is being damaged by Snake's aging, and unless he kills himself long before he dies "naturally," the virus will lose its ability to differentiate between the people it was coded to kill and the people it was not, meaning Snake will cause an epidemic. The second problem is solved so Snake doesn't have to kill himself to stop the epidemic, but the first problem is most assuredly not, and the only reason we don't watch Snake die on-screen is because the ending fades to black instead of fast-forwarding six months.
Mass Effect pulls some good ones. First, the set-up; all spacefaring races get into space by use of Element Zero, which, when hit with electricity, alters the mass of matter temporarily (the eponymous mass effect.) Interstellar travel is based on the mass relays, giant mass-effect devices left behind by Precursors who vanished fifty-thousand years ago.
Mass Effect:The Precursors found the mass relays just like the current civilizations did, because they were left behind by a race of sentient machines who return to the galaxy every fifty thousand years and destroy all intelligent life. Because interstellar society functions based on the technology they left behind AND CONTROL, they have little trouble in the act and the galaxy is powerless to resist. This is actually a cycle of extinction, and based on evidence dating back millions of years, the cycle has repeated over seven hundred times.
The oldest sign of resistance is a corpse of one of these sentient space ships. From 37 million years ago. There is, however, NO SIGN ANYWHERE of the civilization that did it other than the crater left by firing the weapon. To put it in perspective, The Precursors referred to above were only about 50,000 years ago...
Mass Effect 2:The cycle of extinction is the Abusive Precursors' reproductive cycle. They build their babies by turning a species they exterminate into genetic paste and using it for building material.
Also the species that are not suitable to be turned in Reapers, are turned into mindless slaves. We find this out with the Collectors which are actually Protheans.
Mass Effect 3:The Reapers exist to ensure that some organic life (the non-space-faring life they skip during each cycle) will always exist somewhere. They were created with the belief that if any society is allowed to continue existing beyond a certain point after discovering interstellar travel, they will eventually create synthetic life, who in turn will eventually turn on their creators and wipe out organic life. The death they bring and the atrocities they commit is something they believe necessary for organic life to exist at all.
The series' original writer had laid foreshadowing for an entirely different awful truth to be revealed in the third: that the mass-effect is effectively poisonous to the galaxy and causes the stars of populated systems to die long before their time. The Reaper Cycle in this version is a stop-gap measure, slowing the effect to a semi-controlled crawl until a solution could be found.
In the final chapter of Mother 3, Leder's final role is to tell Lucas the truth about his beloved, idyllic hometown of Tazmily. It was always just a fabrication. A final outpost for humanity, perched on the edge of nothing, populated with the last remnants of humankind, who had been willingly mind-wiped and built a false Arcadia in order to prevent a second Armageddon.
In Silent Hill 2, after barely making it to the hotel where he and his deceased wife spent so much loving tie together, James finally realizes that he killed her, and that the guilt of whether it was to spare her suffering or to move on with his life has driven him insane, and all the horrors he saw were a combination of his own psyche and the malign forces behind Silent Hill destroying him.
Worse yet, given his father's statement in Silent Hill 4 (James didn't return from Silent Hill), it seems that the ending where James kills himself may be the true ending, though given that the law may be less than forgiving for the murder he committed, he may simply have gone into hiding, possibly with his new foster daughter.
In Cross Channel, this is how Taichi finally breaks Youko down. The awful part wasn't the fact that they killed 14 people at the Shinkawa mansion, it was the fact that Youko didn't kill a single one of them.
In Star Wars: Knights of the Old Republic, the Jedi Council prevent the other party members — and the player character him/herself from realizing that s/he is an amnesiac Darth Revan with a reprogrammed personality.
Corpse Party: Naomi is already in bad shape from Seiko's suicide... Then she finds out that Seiko didn't commit suicide, Naomi herself killed her. We later find out that it was only Seiko's text that kept Naomi from crossing the Despair Event Horizon.
In Diablo III, Templars of the Templar Order are convicted criminals who are tortured to "cleanse" them of their sins and then mind-wiped so that they can be turned into weapons against the darkness with purpose and clarity. When Kormac, your follower who hails from this order, comes across the journals of Jondar, a turncoat Templar who you help him kill when you recruit him, and reads the "key words" that act to restore his memory, the Awful Truth is revealed. It turns out the Order doesn't really give a damn about the guilt or innocence of its initiates, and will gladly pile false sins upon an innocent, as they did to both Kormac and Jondar, if they deem him to be a worthy asset to the Order.
And then it all got worse. It turns out that the real reason Adria wants the souls of all seven of the Great Evils put into the Black Soulstone isn't so that she can destroy them all forever in vengeance for what happened to Tristram — it's because Adria pledged herself to Diablo's service long ago and seeks to bring about the rebirth of her master as the Prime Evil, the embodiment of all seven of the Great Evils in one being, in accordance with Diablo's grand plan. And the vessel that she uses to bring about this rebirth? Her own daughter Leah, whose true father turns out to be none other than Diablo himself by way of the Dark Wanderer, a.k.a. the Warrior from the very first game who got himself possessed by Diablo after sticking the fragment of the demon lord's soulstone into his head.
Brothers in Arms: Hell's Highway: You remember that scene in the first game, where a distraught Leggett essentially killed himself by firing at an enemy tank with a pistol while screaming "TAKE ME!!!" until he got blown up? Turns out that Baker indirectly caused that when he attempted to protect Leggett from the others by telling him to keep the secret that Leggett was responsible for Allen's and Garnett's deaths when he caused that fight that alerted the enemy patrol, since the other squad members may have tried to kill Leggett for causing the deaths. The burden of keeping the secret, coupled with the fact that Leggett's telling no one about it made the other squad members think that he hid in the bushes like a coward while Allen and Garnett died, therefore making them hate him anyways, was too much for the poor guy, which is why he charged the tank in the first place.
Mad Father: Subverted at first; it's no secret that Aya's father is a psychopathic murderer having an affair with his assistant (Aya's narration after the opening cutscene actually starts with "I know father's secret"). But there's another awful truth that she's not aware of, which her mother reveals at the very end as a last resort. It basically sums up as "Well Aya - there's good news and bad news for you. Bad news first: your father's 'research' was all practise so he could eventually turn you into a doll and keep your for himself forever, and he murdered me when I threatened to run away with you. Good news: you're getting a pretty new dress too!
BlazBlue centers the development and deconstruction of Noel Vermillion around this trope during Continuum Shift. During her encounter with Terumi, Noel goes berserk after realizing he used and tormented Tsubaki, voluntarily lifting the seal on Bolverk with the intention of obliterating him. After feeding off her hatred and pushing her to her limit, Terumi feeds her the history of the Prime Field Devices in graphic detail - up to and including that she is one of them. The relentless input is too much for her to bear, and she promptly breaks down, left prone for tempering into Mu-12.
In a surprising use of this trope in a reconstruction, Slight Hope ends with a double serving of it. In addition to learning that Noel is a Prime Field Device amidst a graveyard of her 'predecessors', Makoto learns from Rachel in the very next sentence that beastkin like her were also made by human hands. Unlike Noel, however, Makoto does not break, and in fact uses the experience to strengthen her resolve to save her friends.
NieR has several ones revealed throughout multiple playthroughs, but the main one involves the main mooks, which are called Shades. The game is designed in such a way that you'll probably have killed several hundred Shades (it can feel like a lot more than that) by the endgame, and you don't really give it much thought. The main character eventually develops a psychotic fixation in killing them as a response to the tragedies that plague his life. Towards the very end of the game it is revealed that the shades are actually the remnants of the real humans who underwent a process to clone their bodies which were being dissolved due to a mysterious disease, and the people you thought were humans this whole time were just clones of them; the main antagonist of the game, the Shadowlord, is actually the original Nier who wants the exact same thing you do. It's implied somewhat in the first ending, but subsequent playthroughs explicitly show that most of them are entirely sentient...which basically makes you a mass murderer. Supplementary materials and Word of God also reveal that by the end of the game your actions have doomed the human race.
In Bastion, Zulf was an ambassador of the Ura in Caelondia before the Calamity, and was working in an apparently successful effort to promote peace between the two peoples. He was also Happily Married, but then the Calamity happened, which killed his wife and all but destroyed Caelondia. He was almost Driven to Suicide after The End of the World as We Know It, but then you come along, and you and Rucks give him some hope that you might be able to fix things. But then he finds Zia's father's journal, which fleshes out the Calamity's true purpose. The Caelondians built it, as a weapon of mass destruction with which to wipe out his people, meaning all of his past work promoting peace was effectively useless. He also finds out that Rucks was one of the people spearheading the project. He promptly flips his shit and does a Face-Heel Turn.
In Kingdom Hearts Dream Drop Distance Xemnas and Xigbar reveal to Sora that the Nobodies of the Organization were regaining their hearts all along, and they were lied to and told they had none. On top of that, they thought they were trying to complete Kingdom Hearts to gain their hearts back, but in reality, once they completed it, Xemnas planned to use it to strip them of their new hearts and turn them into Xehanort clones.
Ys Seven has returning Ys hero Adol arrive to Altago and by a series of events, becomes a Dragon Warrior. Simply enough, he goes around the land to visit the shrines and collect the blessings of the Dragons, especially in the growing phenomena that's been happening (giant monsters appearing more commonly, Iskan fever outbreaks, ect.) Two curve-balls come your way though; first is that The Ace Dragon Knight Scias and Innocent Flower Girl Tia are the Big Bads of the story, who framed you for killing the king in the first place. A little later, the Moon Dragon warns you that what he'll reveal if accepting to fight and win, you're not going to like. The fate of Altago is that it always faced a Reset Button whenever the balance of the land was broken. The necessary action to fix all the phenomena is to start anew, which the Iskan Elders are always tasked with. The Dragons select a Dragon Warrior to stop this as a proxy for the life on Altago... but only out of courtesy. It's almost expected/guaranteed that the Dragon Warrior will lose, even with the Dragons' blessings, as it has happened an untold number of times before since Altago was first made.
In Dragon Age, the Grey Wardens are all doomed to become Ghouls. Their variation of the Taint just takes a lot longer to change them than the normal version. The reason Grey Wardens are the only ones who can slay the Archdemons and end Blights? An Archdemon can resurrect itself by transferring its soul to the nearest Tainted being, which is normally a soulless Darkspawn. If that being happens to be a Warden instead, the soul of the Warden and the Archdemon will destroy each other. The Wardens don't tell anyone these secrets until after they join the order, since no one in their right mind would join them if they knew.
Subverted in the first Ace Attorney game near the end of case four: Edgeworth reveals to Phoenix the reason he's become so bitter over the years is that he accidentally killed his own father as a child. Phoenix, however, can't believe that, and soon proves the killer was someone else (in fact, it was Edgeworth's adoptive father, making what should have been an Awful Truth for Wright into one for Edgeworth instead.)
In case 2 of the second game, the Awful Truth is that Morgan Fey, Mia and Maya's aunt, is scheming to get Maya framed for murder so that her own daughter, Pearl, can become Master of Kurain village (although Morgan herself is not the murderer). This is hard enough on Mia and Maya, who loved their aunt, but it's even worse for Pearl herself; Mia arranges to have Pearl channel her during the second day of Maya's trial so that she won't have to see Morgan being exposed as an accomplice.
Little Busters!: In Komari's route, that she had an older brother whom loved her but who died when she was little. In Refrain, that the world the characters are in doesn't exist - it was created after a terrible bus crash left nearly all of them with fatal injuries and was designed specifically to make Riki and Rin strong enough to be able to handle the truth and live on their own afterwards.
Girl Genius, when Agatha discovers her mother Lucrezia was "The Other" who ruined or zombified about half of Europe. Bonus points for off-handed delivery. Later Agatha herself supplies a few missed memos to an impostor pretending to be her. Right after the only scene when Zola acted nice, at that.
A side story shows a guy in apparently his dream life: a great apartment, nothing to do but play games, and endless, tailor-made sexual partners. Odd things keep happening and he is driven to find out that he's actually in Hell and that, once he knows this, he can never return to the carefree life he had been living and instead will exist for eternity as a obscene, crippled husk. Worse still, he finds out by running into one of the hundreds of other damned souls whose fate he now shares.
In the short story "How To Make A Monster", we see how Drip ended up as the Sin of Lust. The final act that dooms him to this role? He's taken back in time and told to kill two people. These people turn out to be Drip's own parents. That's right, the event that doomed Drip to be raised by his grandmother, who sexually abused him for years and would be the catalyst that would send him towards the path of a serial murderer and rapist... was something that he did himself after he'd been condemned to hell. The most terrible part? He didn't realize who he was killing until after he did it.
Everything that's [REDACTED] or [DATA EXPUNGED] on the SCP Foundation is to prevent the general public from learning what they keep locked up. Most of the time, it's for the best (see Procedure 110-Montauk).
Hank discovers that Dermott's sister who he just had sex with, was really his MOTHER, and that Rusty was his dad. Yes, he had sex with his half-brother's mom. Fortunately, Sphinx is right next door with the mindwipe machine! Hank cheats on it a bit by leaving himself a message saying he had sex, but leave out the Dermott's mom part. And makes a Total Recall joke at his own expense.
The identity of Hank and Dean's mom is strongly implied to be this.
Hank and Dean themselves stumble into a lab full of clone-slugs of themselves suspended in vats and drop in a catatonic blackout. Their dad manages to convince them they saw their Christmas presents of an army of robot slaves. In the prequel to Season 5, it looks like Dean is catching on to what they really are.
Triana has a portal to an extradimensional realm in her bedroom closet, and gets repeatedly mindwiped by her father every time she forgets.
Two-Ton 21 is not really seeing 24's ghost, but is just hallucinating him out of grief and guilt.
Played for laughs and subverted in The Simpsons episode "Brother's Little Helper". When Special Guest Mark McGwire admits that Bart was right and Major League Baseball is behind a conspiracy that is watching everyone, and they ask him why, he replies, "Do you want to know the terrifying truth, or do you want to see me sock a few dingers?" They choose the latter option.
On the Straight Dope forum, several members shared stories of how, when they were children, they'd been told that their mysteriously disappeared pets had been "sent to live on a farm." Cue the inevitable post that went along these lines: "That's a coincidence, because when I was little, I had a dog that was sent to live on a farm.... oh ^#@$% I need to call my parents NOW."
As many a vegetarian will relate to you, many children are told that meat simply comes from the store and don't think about it any further.
Quite possibly apocryphal: the school of Pythagoras was so shocked to discover that the square root of 2 is an irrational number (i.e. cannot be expressed as fractions) that they kept the knowledge a closely guarded secret, and people who leaked it were punished by death.
The Atheist Experience deconstructed this when a caller asked "What's wrong with a comfortable delusion" by arguing that the trauma isn't caused by finding out the truth, but by discovering you were lied to. How many of these examples would have turned out better if the people telling the lies had just told the truth in the first place?