Most heroes have a Deep Dark Secret of some kind hidden somewhere in their past. It seems to be something of a job prerequisite, as well as providing an easy jump-off point for character development. Reveal the secret, and hey presto! Suddenly everyone looks at you a little differently.
On occasion, the Deep Dark Secret will come as just as much of a surprise to the hero as to their fellow cast. This is especially true if they've been the target of Laser-Guided Amnesia, memory-wiping magic, or (more usually) have just never been told about it.
There's that. And, then, there's Locked Out of the Loop.
In Locked Out of the Loop, most of the main points still stand. The hero still has a Deep Dark Secret, and is still oblivious to it. The catch is, every other significant main character is fully aware of the secret and its implications, and they're all collectively conspiring to keep it hidden from the hero - either for the hero's own good or because it's crucial that the hero not know for some reason.
It hardly ever works. If they're lucky, though, the hero won't hate them too much when it finally comes out.
A favorite and none too successful technique so that he will not Turn Out Like His Father. Unfortunately, this usually results only in the mysterious parent taking on the allure of Forbidden Fruit — which may result in a harder than usual crash.
See Tell Me About My Father. Compare Metaphorically True, a common method of obscuring the loop, and You Didn't Ask, where the person in question could have resolved everything for themselves by just posing a few queries. Can lead to It Seemed Trivial, when someone who knows something is Locked Out of the Loop, and doesn't know the importance of his knowledge. Compare Unwitting Muggle Friend.
If people think a character is Locked Out of the Loop but they turn out to have known all along, you have a Secret Secret Keeper.
They also must keep it a secret that they are an alien, a time-traveler and an esper because they fear if she had proof they existed, she would subconsciously create more of them, or even stranger beings, or who knows what else might seem "fun" to her.
In fact, the idea that Haruhi is God incarnate is just what they think Haruhi's secret is. Or rather, it's what Kyon and most of the readers think, thanks to Itsuki "Completely Trustworthy" Koizumi. Yuki and Mikuru's factions have their own theories. They're all keeping watch on her because none of them are entirely sure what she is or what she's capable of, but they're all pretty confident that letting her find out about and/or overuse her powers would be very dangerous.
There's the entire adult population of the village concealing the fact that the eponymous main character had the nine-tailed demon fox that nearly destroyed the village sealed inside him, so he could live a 'normal' life. It didn't work. He just thought they hated him for no good reason instead. Although it did work with the children of the village (which was probably the Third's intention). While Naruto was never very popular, his peers lack the naked fear of him you see from the kids Gaara tried to befriend in his flashbacks.
Another loop they tried to keep Naruto out of was the fact that Tobi/Madara and Kabuto decided to declare a fourth world war. Justified in that they kept it from him to protect him, as Tobi's goal was to capture the Hachibi and Kyubi. Everybody figured that if he was aware of the war, he'd rush to the front lines to fight Tobi. Guess what Naruto does when he does find out about the war.
Naruto gets this a lot. Several important figures didn't tell him that His father was the Fourth Hokage, and His mother was the previous jinchuuriki, information that would have come in handy earlier than when it was actually revealed.
Ignorance runs in the family as the newly revived Minato knows nothing of Orochimaru's attack on the village, the conflicts between the Uchiha and the Senju, or that his student, Obito, was the one who used the Kyuubi to attack Konoha and cause the death of himself and his wife. Though he has been dead or not even born for most of these revelations. As for Obito, Minato, understandably, thought he was dead.
In the Shippuden movie Blood Prison, Naruto is locked out of the loop about the mission he was assigned to without his knowledge until AFTER the mission was concluded. Which means he was seemingly abandoned by everyone close to him, locked into a prison, and suffered both physical and emotional torture without knowing WHY.
Misaki from Kidou Tenshi Angelic Layer is locked out of the loop about her mother's real whereabouts until the very end of the story. This is a spoiler for the manga, but is revealed early on in the anime.
Blood+: Both Haji and David adamantly refuse to tell the amnesiac Saya anything about her past, insisting she has to remember on her own. Unfortunately, this results in them forcing Saya into horrific bloodshed and several Break the Cutie moments without even knowing why.
Lillia of Allison and Lillia is a shining example: she is the only member of the main cast unaware that her childhood friend Treize is a bona-fide Prince, and that her dead father is still alive under an assumed identity, and a spy... oh, and dating her mother. Considering the fact that both of these things make her a potential assassination/kidnapping target, you'd think someone would be nice enough to clue her in, but instead, they actively keep this information from her.
It takes a villain forcing him at gunpoint to finally make Treize reveal his true identity to her. Later he comments that he would have preferred it if she had never found out… even though their relationship was already becoming increasingly serious by that point. She forgives him, but it still seems like a very disrespectful way to treat the one you love.
In Tsukuyomi Moon Phase, male lead Kouhei (and the audience) is led to believe that his immunity to ghost attacks and his inability to see them at all was because he was "Spiritually retarded" and possessed no spiritual powers unlike his immediate family. It is eventually revealed that he is, in fact, an incredibly powerful psychic whose abilities were sealed for his own protection when he was a baby, at least partly by telling him repeatedly that he had no powers. Even in this sealed state, however, he was powerful enough to banish evil spirits by denying they were even there.
Botan, Yusuke, Kurama, and Koenma (and in the anime, Shizuru) know that Yukina is Hiei's sister. Whether or not Yukina has figured it out is left as an exercise for the audience (she calls Hiei "brother" at one point, then backtracks and says she would like her brother to be like him), but Kuwabara definitely doesn't and Hiei will probably kill you if you change that.
Kuwabara thinks this is in play when he's the only one who doesn't realize Genkai was dead until he fights Elder Toguro in the Dark Tournament finals, and believes that he was left out because they think he would be scared off if he learned the truth. Kurama tells him that Yusuke didn't tell anyone else, and Yusuke says that he merely couldn't bring himself to say it and admit that it was true.
Tatsuki has just enough spiritual awareness to know that something's going on, just not what. Does she ever get pissed when Ichigo refuses to tell her. He doesn't come clean to his friends until after the Arrancar arc.
Byakuya ordered everyone in his estate not tell to Rukia the real reason why she was adopted into the Kuchiki family. Rukia thought it was because she resembled Hisana, Byakuya's dead wife, but it was actually Hisana's dying wish for her husband to adopt the younger sister she had abandoned in the Rukongai.
Ichigo didn't find out Urahara was actually former captain of the Soul Society's Twelfth Company, who was involved in the creation of the item Aizen staged the entire plot to obtain and used Rukia to hide said item until AFTER the Soul Society arc because Kisuke believed Ichigo would then refuse to go along with his plans.
Souken knows why Ryuuken has rejected the Quincy Clan and even his own powers, and accepts that decision though it pains him greatly. Neither Souken nor Ryuuken, however, will explain this to Uryuu, which has resulted in nine years of nasty estrangement between Ryuuken and Uryuu. Souken does strongly imply, however, that Ryuuken is in some way trying to protect his son… Uryuu is about the only person on Earth to whom this is not immediately obvious.
Urahara also neglects to tell Orihime that Aizen is after her powers, instead telling her that she isn't suited to fighting. She goes to Soul Society with Rukia to train because of this, which leads to Aizen ambushing her as she travels between the two worlds. Orihime is then forced into a very cruel Sadistic Choice that kicks off the Arrancar Arc. Nice Job Breaking It, Hero.
Isshin keeps the fact that he is a former Soul Reaper Captain secret from his family for 15 years. When Ichigo first finds this out, he just says that his dad must have had his reasons and is content to wait at least another year and a half before hearing the full explanation.
At least three major villains all know and have outright told Ichigo that there is a lot about his family's past that he's still completely unaware of, and mock him for his lack of curiosity and insight.
Major plot point in the first arc of Higurashi. Keiichi's friends don't tell him crap, so he gets paranoid and bludgeons them to death. They just didn't think it was much of a deal to tell him... and holy crap they were wrong.
Guld in Macross Plus, who sexually assaulted his ex-girlfriend Myung but due to trauma and drugs used to suppress his aggressive Zentradi nature he's forgotten most of it, other then the image of his friend Isamu with the partially disrobed and crying girl... so he thinks that Isamu was the rapist. Not exactly made better by how the also emotionally broken Isamu and Myung actually decided to not tell him anything about it.
The second season of Code Geass opens with Lelouch suffering from Laser-Guided Amnesia and an entire government surveillance team camped out at his school to keep it that way. Predictably, that doesn't last long.
Minato is a Heroic Bastard, and raised by a domineering mother that refuses to talk about his father. Almost every single other character in the series seems to be aware of the obvious, which is that Big Bad Minaka Hiroto is his biological father. Even his younger sister and several of his enemies are aware of this fact, but no one seems interested in letting him in on the secret. The subject is often avoided or ignored, and an omake reveals that he once attempted to ask his mother to Tell Me About My Father. She strictly forbid any discussions of his father in the Sahashi household from that day forth, and he simply accepts that his father is "dead or something", completely unconcerned about learning more. Not even Kazehana mentioning in a wistful fashion how much he looks like his father is enough to make him curious, even when she admits to the identity of the man that broke her heart.
Miya, his terrifying landlady, is very strict about keeping under wraps the fact that she is Sekirei #01, and hinted to be a goddess. Almost every single one of her other tenants, including half of his harem, are aware of this fact; they've simply been threatened into silence, and work very hard to keep Minato from learning the secret. Miya even jokingly (we hope) threatens to kick him out if he ever learns her secret. This turns out to be an empty threat, as he takes learning her secret in stride and remains respectful of her neutrality in the Sekirei Plan. She becomes a vital source of information, and remains a trusted mentor to the group.
Renton suffers a lot from this in the first season of Eureka Seven. Since he's technically a full member of Gekkostate, he ends up getting involved in a lot of missions without being informed as to what exactly is going on... and then the others (particularly Holland) actually blame him when he messes things up.
Shinji Ikari the main character in Neon Genesis Evangelion, who for the most part is very unaware of the shady going-ons behind the scenes of Nerv, despite the fact that he has a very important post inside the organisation as a Humongous Mecha pilot. His friend, Kensuke, is quite shocked to learn this fact, as he finds out that Shinji can't neither confirm or refute any of the rumors he hears through his own sources in the organisation, as Shinji honestly knows next to nothing.
It all comes to a head as Misato Katsuragi a decides it wouldn't be a good idea to tell Shinji that the fourth child is Toji, his best friend. When she does try to tell him, her message gets cut off just at the last moment. He ends up finding out in the worst possible way: he sees the heavy injured Toji in the remains of the Eva 3 plug which Shinji had just been forced to crush with his own (Eva's) hands.
In Elemental Gelade, Coud was informed that Edel Garden, the place Ren was planning to head to, was a very dangerous place and warned never to bring her there at the end of vol 8. Coud decided to go ahead anyway without telling Ren.
In Great Teacher Onizuka, Onizuka was informed by the hospital doctor that he would really die if his head suffered any further serious blow. He ended up not telling anyone about it in order not to cause any worry, but some students found out anyway through the doctor.
Due to Mustang's plan to smuggle an accused Maria Ross to Xing in Fullmetal Alchemist, her partner Denny Brosh wasn't told of her true fate until late in the final arc (though for good reason, as he couldn't lie to save his life). Her parents were also excluded on her request.
And in a more minor example, Mrs. Bradley never had a clue that her husband and son were Homunculi until after the final battle.
Soul Eater has a couple. The existence of the Kishin to everyone who isn't Shinigami or Asura himself. Everyone else gets a watered down version they can deal with - Spirit's early version of the meister who gave normal souls to his Weapon fits neatly as a warning tale to students to follow the rules and be brave. The Death Scythes get their initial instructions on the basis of Asura being a potentially dangerous monster in hiding. The truth, for the moment, appears to be a good deal more complicated and deranged. Kid gets a personal lockout regarding his origins, as until the very end of the series only Shinigami (and possibly the teachers, but definitely Spirit) know what Kid is, and what Shinigami intends for Kid to do.
Kozue, from Mahoraba. Every single person at Narutakisou knows about her disease. Except for her.
In Romeo X Juliet, the Capulet sympathisers keeps Juliet's true identity as the last heir to the throne a secret from her until her sixteenth birthday. Considering that the story is based off a tragedy, this turns out to be a horrible, horrible idea.
In Tiger & Bunny, Kotetsu's daughter Kaede is the only member of his family that's unaware that he's a superhero. Word of God says it's an attempt on his part to protect and not worry her. While the secretiveness is a Fatal Flaw on his part, he might have something of a point as the very first thing that Kaede does after discovering her father is Wild Tiger is run off to Sternbild alone to try to save him.
The sisters in Magikano are quite persistent in making sure Haruo doesn't use any magic or realize they're witches.
Hitomi Shizuki from Puella Magi Madoka Magica is never told that her best friends Sayaka and Madoka, as well as their classmate Homura and their sempai Mami, are involved in the whole Magical Girl stuff. This bites Sayaka in the ass later.
The eponymous Magic Knights of Magic Knight Rayearth are greeted by Guru Clef, the only person besides the Pillar who knows all there is to know about the job. Depending on the translation, he gives them and Presea a technical truth about fulfilling Emeraude's wish or a Motivational Lie about restoring her rule. The true "legend of the Magic Knights" is that Emeraude summoned them to kill her, fearing that her love for Zagato would destroy Cephiro since it distracts her perpetually from her Pillar duties, which she cannot resign from unless it's through death. A triple Heroic BSOD ensues when this is revealed and the girls are forced to kill Emeraude.
When Coach Munakata dies in Aim for the Ace!, nobody tells his star pupil/love interest Hiromi because she and the team are in a tournament in the USA, and they don't want her to lose. (Not to mention Todou lost in said tournament because he learned about it and fell in an Heroic BSOD.) She only finds out when she goes back home, and predictably she almost crosses the Despair Event Horizon.
After discovering that Abdul is still alive in JoJo's Bizarre Adventure, Polnareff excitedly rushes off to tell his comrades the good news... only to discover that all of them knew this and just decided not to tell him because he sucks at keeping secrets.
In A Certain Magical Index and its sister show A Certain Scientific Railgun, the heroes often leave their loved ones in the dark about their adventures despite working and fighting side by side with them in others. In addition, hardly anybody in Academy City knows that magic exists.
It happens in a dark yet oddly amusing way in Gundam Age. When one of the Vegan pilots psychic abilities goes out of control she starts causing massive feedback to all other psychics present as well as takes control of their mecha and makes them all start attacking each other, both her friends and foes. In between cuts of the psychic pilots groaning and yelling at her to stop, we see cuts of Asemu, the only guy there who doesn't have psychic abilities so is unaffected by all this, who has no idea what the hell is going on.
In Attack on Titan during the 57th expedition beyond the wall, the Survey Corps run into many problems once the Female Titan shows up. After it's captured, Eren and a few others discussed what happened and he realized that even some of the veteran troops were unaware of the plan to capture her. However, this was because the plan was made due to the high possibility that there was a spy within their ranks. This also explained why different groups were told different things before they headed out, such as where Eren was in the formation so it could be narrowed down who was leaking information.
It's also the cause of the higher-than-usual death toll of the expedition as all the soldiers thought they were fighting a normal titan. If they had known, as Erwin had, that it was an intelligent titan they would have used significantly different tactics.
In the final episode of the 3rd Tenchi Muyo! OVA, we come to find out that Tenchi's own mother imposed this one him concerning her passing, deciding to use her death as a massive joke. When Katsuhito and Noboyuki went through with it, Tenchi was more than a little pissed. To be fair, though, a lot of Tenchi's heritage was this to him.
Comic book example: Flycatcher in Fables is constantly searching for a way to return to the Homelands to find his wife and children. Everyone else in the Fabletown office knows, from his ramblings whenever he's drunk (which he forgets completely afterwards) that his wife and children were tortured, his wife and daughters in fact raped in front of him, and killed when his kingdom was invaded, but they let him believe they're still alive for his peace of mind. There's some evidence that magic is being used to keep his memories suppressed.
Recently, Flycatcher regained his memories, and was last seen having something of a breakdown and lashing out at Santa Claus, who restored them.
Early on, Zoot the shrew was so nearsighted that he didn't realize he was sharing the margins of Cricket magazine with insects and other invertebrates. Everybuggy else carefully nurtured his belief that he was hanging out with moles, rabbits and other small mammals, because shrews normally eat bugs. (Zoot later got some glasses and learned the truth, fortunately after he became a vegetarian.)
Kup of The Transformers IDW was once marooned on a planet with radioactive crystals. The crystals caused him to view other Autobots as vicious zombies, leading him to brutally slaughter several rescue parties. He was ultimately saved, but had to be constantly be fed modified doses of the crystals to keep the hallucinations at bay. Everyone aware of what happened was sworn to secrecy to avoid burdening the ancient bot with guilt of having killed his own comrades.
Knuckles' Guardian lineage, the number of echidnas still around and his family in general in Archie Comics' Sonic the Hedgehog, at least pre-Sonic The Hedgehog Mega Man Worlds Collide. Up until Robotnik's Ultimate Annihilator went off, Knuckles thought he was the last of his kind, save for the power-mad Enerjak. Then, the Dark Legion came knocking. Then Echidnaopolis showed up, with his mother there still alive. Within a year, Knuckles would also find out about the Guardians and their purpose and that his dad was alive.
This is Batman's schtick, especially during the period between the late 1990's to the mid 2000's, to the point where things would blow up spectacularly because he never bothered to tell people things at all. Some of the worst case scenarios include his backup plans against the Justice League (they were meant to be secret and he didn't want anyone to know... until Ra's al Ghul got them), his gang-controlling plan (He purposely locked Stephanie Brown out from it because he adamantly distrusted her) and not outright telling the Bat-Family that he might have let The Joker know that he might know their identities (how was he supposed to know he'd figure it out?)
Dad: Yes, we're well aware of his reputation. Fortune Teller: And yet, you do not know him at all. Dad: I'm sorry? Fortune Teller: You only see what you choose to see, and you see only the negative in your son's persona. You are blind to what he sees.
Also, Socrates is the only one of the five protagonists to not know about his transmitter chip. This is finally subverted in Retro Chill, as Calvin tells him about it, much to Sherman'snote the one who placed it there in the first place horror. He reacts about as well as you'd expect.
In A Delicate Balance, Applejack is the last pony to find out that Twilight has a crush on her. Spike is (inadvertently) left in the dark about Twilight's crush for even longer, and he feels rather slighted that no one thought to tell him.
In Dirty SympathyPhoenix and Trucy does not know that Klavier and Apollo made a "Strangers on a Train"-Plot Murder to get rid of their abusers and they both knew each other before the Witaki trial. Trucy never finds out about the former, but she eventually found out about their relationship and realized on her own that they had been together longer than they said they have. While Phoenix saw they had feelings for each other, he didn't know they were already together. He finds out about the plot when he accidentally asked an Armor-Piercing Question and Apollo flees the country. Both Trucy and Apollo never find out that they're siblings because by the end Apollo fled the country, never to return and Phoenix feels it would be too cruel to tell them.
In Dark Victory, Bette Davis's doctor and friend decide to not tell her that her surgery failed and her brain cancer is terminal. She is super-pissed when she finds out.
In Moulin Rouge!, the theatre cast hide Satine's imminent death from tuberculosis so she can clinch a deal with the Duke.
In A Scanner Darkly, Bob Arctor's police superiors know his identity even though his Substance D abuse has split his personality to the point where he thinks Bob Arctor is the man he's chasing and that his undercover identity, Fred, is his real identity. His reaction is not overly positive.
The Skywalkers in Star Wars are basically ruled by this trope.
This seems to be a common theme in Star Wars; see Knights of the Old Republic for an even more extreme example - accompanied by an ironic lampshade hanging if the amnesiac Darth Revan tells Carth "you were born out of the loop."
Early in Return of the Jedi, C3PO is clearly unaware of the whole plan unfolding around him regarding Jabba the Hutt. Compare R2D2 who was carrying Luke's lightsaber the entire time to give to Luke at the right moment. Presumably, this was because the heroes thought C3PO being made aware of the plan would have made it much less likely to succeed.
Walter Sobchak: Were you listening to The Dude's story, Donny? The Dude: Walter... Donny: What? Walter Sobchak: Were you listening to The Dude's story? Donny: I was bowling. Walter Sobchak: So you have no frame of reference here, Donny. You're like a child who wanders into the middle of a movie and wants to know... The Dude: Walter, Walter, what's the point, man? Walter Sobchak: There's no reason - here's my point, Dude, there's no fucking reason why these two... Donny: Yeah, Walter, what's your point?
Goodbye Lenin: Alex tries to hide the fact that the German Democratic Republic is gone from his mother, who was in a coma when the Berlin Wall fell. And it turns out that his mother has kept a secret of her own from her two children - Their father didn't leave for the West because of a woman, he left because of harassment he received for not joining the Party, and he planned for his family to join him in West Germany. He even sent scores of letters which his wife hid behind the cabinets.
36 Hours (1965): Just before D-Day, the Germans construct an elaborate hoax involving an entire cast of English-speaking German spies in a fake hospital, all to make a captured American intelligence officer believe that he has had amnesia and the war is in the past. Their motive is to get him to reveal details of D-Day as part of his "therapy".
Friendship: Veit's father never made in to San Francisco, but died at the Iron Curtain. The postcards were sent by a proxy of the state security.
The Truman Show is a classiccase. Truman's life is being aired 24/7, and he's the only one who doesn't know it. Everyone he's ever met has been an actor paid to keep the secret.
Pops up in the classic romance film Love Story, when the doctors and the husband decide to just not tell the wife she's terminally ill, right up until it's blatantly obvious she won't be getting better.
In David Eddings' Belgariad, it is feared the sorcerer Belgarath has lost his powers at one point. The remaining sorcerers keep the information secret so the neighbouring countries won't invade and because the magic in this universe is based partially on one's self-confidence — if you don't believe it'll work, it won't. (Therefore, while Belgarath might have lost his power if he was left in the dark, he definitely would have had he been told.) Later on, it is shown that he's perfectly fine, and is actually rather surprised at the idea.
Also possibly a subversion in that Belgarath is fully aware that Polgara and Belgarion are hiding something from him - he's just not sure what, although he's pretty sure it's going to be something important. An additional possible subversion is that he's not terribly bothered when he finds out what they were hiding - he understands exactly why they were doing it.
Garion and Ce'Nedra's 'courtship' could be viewed as a masterfulsenselessly negligent arrangement of keeping the concerned parties in the dark until it was too late to run. Polgara, an excellent manipulator, ensures the two spend time together until they were prepared to admit they liked the other. After a year of being around each other more or less constantly, the bomb is dropped on them: A five-hundred-year-old treaty dictates that the first Rivan King (Garion) to return will have an Imperial Princess of Tolnedra (Ce'Nedra) as his wife. Ce'Nedra was aware of the treaty, but thought the Rivan line was extinct and that the ceremony was meaningless. Garion was not aware of his ancestry or of the treaty. After a predictably bad start, the marriage somehow works itself out.
Garion not being told that he is the Rivan King. Even though he's told he is descended from Polgara's sister at the end of the first book and that there was always only one son of that line... (Retconned in the prequel).
In her introductory book, Princess Ida from Piers Anthony's Xanth series was constantly trying to find out what her magical talent is, only to have everyone who knew tell her it would be counterproductive for her to know at that point. It turns out that her talent is the Idea, where whatever she thinks of will come true as long as the idea originates with someone who doesn't know what her talent is. As soon as she found that out, she stopped being able to grant her own wishes.
Later, it becomes a frequent strategy to bring someone along who is Locked Out of the Loop when you talk to Princess Ida, so that they can suggest ideas that would help the quest along and trigger her talent that way. Usually this is explained to them as soon as they leave Ida's company, even though that means they can't be used for that purpose again. In one case Demoness Mentia, Metria's half-crazy alternate self, has an elaborate plan to free someone from a curse this way.
His Dark Materials, in which it is prophesied that Lyra will change the fate of the worlds (plural)—but only if she doesn't know about her destiny and what she will have to do to fulfill it. Naturally, every adult in her life knows and is busy trying to manipulate her to their own ends.
Ultimately subverted as it turns out, Lyra was hiding and listened to the prophecy when it is told to someone.
In Ender’s Game, Ender is going through an elaborate simulation to help prepare for the coming war, but doesn't know the simulation is going on for real.
Harry Potter suffered from this to a large degree in his interactions with Dumbledore (and, well, everyone). In Deathly Hallows, one of his main sources of angst is the possibility that he might be doing exactly the same to his own allies.
Averted in Order of the Phoenix when Dumbledore explains that there was a prophecy made about Harry that Dumbledore kept wanting to tell Harry about (And Harry had even asked him about in book one), but he had succumbed to the "Old man's error" each year in feeling Harry was too young for such heavy information. Dumbledore then actually does get Harry up to date on things - but only on the things Dumbledore is absolutely sure of at the time.
In Prisoner of Azkaban, Dumbledore, Mr. Weasley, all the teachers, Hagrid, and Malfoy all knew that Sirius Black was Harry's godfather, and they thought they knew that he was partly responsible for the deaths of Harry's parents. Nobody told Harry this.
Harry was told his parents were mundane muggles who died in a car accident and he never even heard of the wizarding world until his Hogwarts letter comes on his eleventh birthday. It's explained later on that Dumbledore wanted it this way. He was afraid Harry would grow up to be a spoiled and useless boy if he was raised by wizards who constantly reminded him of his status as "the chosen one".
The Druids of the Shannara series have a long history of doing this to people they need help from. Walker Boh absolutely hates them for this tendency, and is less than pleased when he realizes that he has to do the same thing when he becomes a Druid himself.
Harry Dresden mentally picks the lock to the loop that Charity is keeping her entire family locked out of.
Harry himself does this to his allies in the first few books. After a few What the Hell, Hero?s from Murphy, he starts to clue his friends in to the full scope of the supernatural world.
The reasoning is rather convoluted, but logical. An abdal, like Darryl, is a channel that passively allows The One's power into the world. If he were told what he is, he could no longer be passive and would no longer be usable as an abdal, so The One's power would leave him. Since that power is the only reason he exists, losing it would mean no longer existing.
Percy Jackson, like Harry Potter, had this problem, extending even to his primary love interest.
In Talking to Dragons, nobody will explain to Daystar who he really is, what he's supposed to be doing with his mysterious magic sword, or any of the backstory involved. Justified in that the sword is being hunted by wizards who can only find it if its bearer knows what it is.
The John Marsden book Looking For Trouble is about a trio of sixth-grader kids who form their own detective club and investigate a suspicious family who have just moved into their neighbourhood. It turns out that the father was on trial for fraud and embezzlement — and that everybody knew, including the kids' parents and some of their classmates. Their parents deliberately left them Locked Out Of The Loop for no good reason, merely saying "We knew you'd find out soon enough".
In Robert Buettner's Jason Wander series, the title character constantly deals with this. He is good friends and works closely with Howard Hibble, a former civilian professor who now works for military intelligence. The problem is that Howard has an obsessive need to compartmentalize information, a habit that working as an intelligence operative has not helped, and feels the need to lie about sensitive information to Jason (who is a very high-ranking officer) at least once every book.
There's a bit of an inversion of this in David Weber's Safehold series. The main character Merlin is the one with the secret, knowledge about the Safeholdian Church of God Awaiting's origins as a Path of Inspiration, but his plan is to eventually make the whole world aware of it. Who to tell and who to keep locked out becomes a significant plot point from the second book on.
Most of the cases its either a case of trust or worrying about the crisis of faith that might be created when a person learns not only is the Church of God Awaiting a Corrupt Church but it was founded as a Path of Inspiration. Then there's Baron Seamount, local One-Man Industrial Revolution, who remains Locked Out of the Loop because his mindset of scientific enquiry is important enough to Merlin's long term sociological plans to outweigh the drawbacks of not letting him have access to Merlin's high tech database.
This happens unintentionally in the Prince Roger books. The entire court knows Roger's father was both a vain fop and a dirty traitor, but it's such a sore topic with the Empress that no one ever brings it up. So everyone assumes Roger's arrogance and vanity are a deliberate attempt to emulate his dad, because surely someone must have told him. Roger, meanwhile, spends his entire life being seen as worthless and borderline traitorous for no reason he can understand. He is extremely pissed when he finally finds out about this.
In The Dark Elf Trilogy, it is heavily insisted that even slaves know who Drizzt's father is. Oh, the supposed father and the real father know it. But when her sister reminds Malice's husband that he has only one son, Drizzt asks himself who is his father.
Read enough Cthulhu Mythos fiction, and you'll be forced to conclude that educated upper-crust Anglo-Saxons are the only people on Earth who don't have a clue that monsters lurk all around them: everybody else, from classical civilizations to backwater native tribes to superstitious blue-collar laborers, knows what's going on.
Jenna isn't informed about Septimus's undertakings very often in Septimus Heap, commonly leading to trouble.
In The Demons Lexicon by Sarah Rees Brennan, Nick's true identity and the fact that it is kept secret from him is more or less what the whole story is about.
In the web-novel Domina, there are five people with powers: Derek, Akane, Laura, Ling, and Lizzy. However, Lizzy is an old friend of Derek and Laura, so they don't want her involved with the screamers and so on. Thankfully, she's kinda stupid, so she doesn't ask too many questions.
The gods, Chiron, and Lupa are keeping a big secret. The Lares of Camp Jupiter, too.
A bit of story hints is that Chiron never mentioned the Roman camp because he swore not to - chances are, Lupa wouldn't mention the Greek camp either.
Nico has been keeping the secret as well; Percy in particular is less than thrilled by this.
In The Hound of the Baskervilles, everybody in Dartmoor seems well aware of the legend of the Hound and its alleged curse upon the Baskerville bloodline. However, the 1742 manuscript that Dr. Mortimer shows Holmes has a closing notation that the author's daughter should not be told about it by her brothers, implying that female Baskervilles have always been kept in the dark about the story.
In "RaisingDragons" Billy Banister is kept from finding who his father really is until part way through the book.
In the Daughter of the Lioness books, the people being locked out of the loop are actually the ones who are the subject of the secret. Sarai and Dove both fit The Prophecy of a twice-royal queen who will take the throne of the Copper Isles from the luarin conquerors. The rebels stipulate that they not be told for their own safety. Dove manages to figure it out on her own anyway, but Sarai (the one they plan to give the crown) remains locked. Which turns out to be a good thing, since she can't keep her mouth shut and winds up eloping.
Live Action TV
At the start of season 3 of House, House is depressed because he thinks he was wrong about a patient; by two-thirds of the way through the episode, four out of the other five main characters know he was right, but don't tell him in an attempt to teach him humility. Eventually they have to tell him as it's affecting his work to the point that he's ready to simply give up the current case.
King Uther in Merlin is Locked Out of the Loop about Morgana's prophetic dreams so that he will not have her executed as a sorceress. All the rest of the main cast knows that she foresaw the Sidhe woman Sophia trying to kill Prince Arthur. Morgana is herself Locked Out of the Loop by Gaius and Merlin, the only ones aware of how powerful her magic ability is; Gaius doses her up with heavy sleeping draught in an attempt to make her forget her dreams.
As of "A Moroccan Christmas", everyone in The Office knows that Angela's been sleeping with Dwight except for Andy, Angela's fiancee.
Lily and Vivian in Pushing Daisies weren't told that Chuck is alive. Olive knows, but thinks she faked her death when she actually died for real only to be resurrected.
Subverted in the (sniff) Series Finale
Londo Mollari is locked out of the loop regarding Centauri attacks on the Interstellar Alliance in Season 5 of Babylon 5 because the other main characters fear he will actually get to the bottom of it and be killed by his own government.
Keeping track of who knows what on LOST can be confusing even for the cast. In one episode, Hurley expresses his frustration over remembering who is in the need to know about what.
Pretty much the entire point of Dark Skies. The backstory was an executive order signed by one president that kept the existence of Majestic and the aliens secret from his successors.
In Kamen Rider Den-O, Ryotaro is locked out from learning that the entire conflict was started by the birth of his Singularity Point niece, primarily because those involved (his sister and her "lost" fiance) actually changed history in order to protect the important thing in question from the Imagin. He only learns the truth by going back in time to before the alteration and posing as his past self to get the information from his sister.
In Stargate Atlantis, the cast uses a retrovirus to transform Michael from a Wraith into a human. His memory is erased as a side effect, and they decide to hide his true nature from him. Needless to say, he is pissed when he finds out.
Keeping Ellie locked out of the spy loop on Chuck turns increasingly problematic as the series goes on.
On Teen Wolf, Lydia. Which is a mistake, given that she's been hallucinating Peter Hale all season.
On The West Wing, CJ is often Locked out of the Loop by the other senior staff on important confidential issues, because if she knows something and is asked about it directly during press briefings, she would be forced to lie to the public, which could jeopardize the White House's relationship with the media. This creates a lot of uncomfortable situations where everyone knows something except CJ, and CJ wants to know the truth, but no one can tell her for her own good. This happens to an extent in real life.
On the Doctor Who sixth season premiere, "The Impossible Astronaut," everyone but the Doctor knows that the Doctor was shot and killed in the middle of a regeneration, so he refuses to be goaded into following the clues they have, since he has no reason to. River Song insisting he must only exposes his mistrust of her, but Amy is able to convince him to do as she asks without question (the implication being that this is reciprocation for her always doing this for him). The following lovely moment is an uncommon expression of mutual respect between the Doctor and one of his companions.
The Doctor: My life in your hands, Amelia Pond.
In series 4, David Tennant's confusion when he first meets River Song is absolutely genuine. Writer Steven Moffat refused to tell anyone where he was going with the character, and David Tennant didn't know any more about her than his character, the Doctor, did.
In The Thick of It specials "The Rise Of The Nutters" and "Spinners And Losers", Malcolm Tucker is constantly kept out of the loop despite being the Prime Minister's spin doctor.
On Quantum Leap, it's eventually revealed that Sam has a loving wife in his own time. This fact is kept from him, because knowing the truth would hinder his ability to cope with leaping from one life to another.
Carl: A month ago?! And you didn't think to mention that when you were here for lunch last week!?
Randy: I got distracted, okay?
In the second season of Star Trek: Voyager, Janeway, Tuvok and Paris all conspire to have Paris act like a malcontent in order to flush out a mole working with the Kazon. They deliberately left Chakotay out of the plan because they suspected the traitor was a former Maquis member, which would put him in an "awkward position".
In the Law & Order: SVU episode "Identity", one of a pair of twins is unaware that she was born a boy, then given a sex-change operation after a botched circumcision damaged her penis. Her parents, physicians, and psychiatrist had kept this a secret ever since, in accordance with the latter's agenda of "proving" that gender identity is environmental, not innate.
Everybody in The Bride Of The Water God knows that Habaek is only a child during the day and regains his handsome adult form at night... except for Soah, Habaek's wife, who is in love with the adult Habaek but thinks he is a completely different person named Mui.
In Assassin's Creed I, modern-day Assassin Desmond was never told that the Assassins are still very much at war with the Templars. His ancestor, Ezio, wasn't even aware of his heritage. Later games make it clear that Desmond was vaguely aware of this while he was a kid in the assassin camp in South Dakota, but couldn't really understand it.
In Metal Gear Solid, Snake believes his team knows more about what is going on around him (Anderson and Baker's deaths, the ninja being Gray Fox, etc.). He is 100% right : everybody was holding back some info so nobody knew who or what was behind Shadow Moses. The Patriots. Liquid wanted to take them out or free Big Boss from their clutches; they didn't give him the chance to try.
In Planescape: Torment, the hero has amnesia. Near the end of the game, you find out that Morte, who has been with you since the introductory scene knew almost everything you had to work so hard to find out.
Also, the reason Dakkon joins up with you so quickly is he has an existing life-debt to you and for all we know was hanging out in the bar because he knew you would be showing up soon.
Something similar happens in Baldur's Gate, lots of people seem to know about your heritage and pointedly refuse to tell you. At most offering vague hints.
In Fire Emblem (the first one released in America), Hector's brother dies, but the secret is kept from him until much later in the game.
In Tales of Symphonia: Dawn of the New World, Lloyd locks his former comrades out of the loop on why he hunts for the Centurion Cores. It's only with the revelation that Emil is Ratatosk that Lloyd decides to reveal why he did so: he was on a task by Martel to collect the cores so Ratatosk can be sealed away before he gets revenge on humanity. Lloyd couldn't risk anyone else on the chance they might let slip the name of the new tree, which would allow Ratatosk to take over and begin his revenge.
Aside from Zero, almost all major characters in Mega Man Zero 3 (Ciel, X, Weil, and maybe even the Four Guardians) seem to know about the truth that Zero (the real one and The Hero) is inhabiting a clone, while Omega is using Zero's original body.
Ciel only finds out in the end of the game, when X tells her. The Four Guardians only as much as suspected, since Harpuia was present when Weil referred to Zero as that body. Of the four, only Phantom knows the truth, since he died fighting Zero in a previous battle and now wanders the Cyberspace afterlife, where all history is gathered.
In Knights of the Old Republic, the player character is running around the galaxy trying to stop the Sith Empire from finishing a war of conquest started by Darth Revan. The secret is that the PC is Revan, with his memories brainwashed out, and that the Jedi Council is trying to use him to uncover the location of the same superweapon that allowed him to begin his war in the first place. No one tells the protagonist all this, of course. Until Malak and Saul Karath find out he's still alive and Malak tells him, that is.
It is sometimes assumed Flandre Scarlet of Touhou Project fame doesn't know she's a vampire, as her maid Sakuya serves her blood under the appearance of normal food. Whether Flandre really doesn't know she's a vampire or not is up to debate, but Word of God says she at least doesn't know how to properly feed on humans. She just blows them up on the spot. All because Remilia won't let her outside, because she had the bad luck to be born with the power to destroy anything by clenching her fist. Cannon appears to joss it though.
Persona4: Both Detective Ryotaro Dojima (the MC's uncle) and Naoto Shirogane (freelance detective) are working on the same case as the Heroes, but the Investigation Team keeps them out of the know for rather understandable reasons. Like many other things in the game, this is Deconstructed:
Dojima's instincts catch onto the MC and the investigation team almost immediately, but he can't bring himself to suspect the person who watches over his daughter.
Naoto is damn well aware that information is being withheld from him, or rather her, and becomes frustrated enough that she resorts to rather drastic measures.
In Jak X, no one wants to tell Rayn that Jak killed her father. Inevitably, she finds out and gets pissed.
In Fallout 3, every adult inhabitant of Vault 101 knows that James and the Lone Wanderer were both born in the Wasteland (even that the Vault was opened in the past) yet they hide it from the kids, including the LW. Of course, he/she ultimately finds out from Moriarty and the rest of the gang gets to know about it when Amata overhears someone saying that they should never have let James into the Vault 19 years ago. Needless to say, they are so pissed that the Overseer declares martial law to try and keep everyone in line. It doesn't really work with the youth demanding to open up to the outside and Vault Security planning to stage a raid on the "rebels" using live ammo without the knowledge of the Overseer. The outcome depends on the player's actions.
Wakka of Final Fantasy X is never clued in on Yuna being half-Al Bhed, and later Rikku being Al Bhed herself. When he did find out, he was not pleased, at first. And then, later Tidus learns that he was also Locked Out of the Loop concerning the fate of summoners when they summon the Final Aeon, i.e. they die. He's furious when he finds out and demands to know why they hid it, but Wakka and Lulu explained that they simply found it too difficult to say.
Tidus also never tell Yuna and the rest about his impending doom if Sin is permanently killed off, until the final battle.
In Vagrant Story, both Ashley (the main character) and Hardin (the Anti-Villain's henchman) are largely unaware of the main plot up until the final cutscenes.
The Legend of Zelda: The Wind Waker: Tetra's mother apparently locked her out of knowing that she's the eponymous Princess Zelda. She also fails to mention why the necklace she gave Tetra is so important. Then suddenly it is revealed that it is a piece of the Triforce, the almighty artifact of the Goddesses, which can grant absolutely any wish when fully assembled.
In Brutal Legend, nobody bothers to tell Eddie who Succoria is, leading him to conclude it was Ophelia and driving her away. Her Face-Heel Turn drives the entire second half of the plot.
Mass Effect 2 does this to whichever human squadmate survives the first game. It's one of the main reasons why the reunion doesn't go so well. Garrus and Tali find out Shepard's alive firsthand, while they only hear rumors about him/her being alive and working for a terrorist organization - which had been leaked by the terrorist group in question in an attempt to isolate Shepard. In Mass Effect 3, fixing this is an important part of getting back on their good side. If the player chooses not to let them back in the loop, it will potentially end with their death because they can't be convinced that it's Not What It Looks Like.
In Castlevania: Portrait of Ruin, Jonathan Morris's father left him the legendary Vampire Killer, but never told him how to draw out its full power. It turns out he was trying to spare Jon the risks involved in wielding it (but apparently not the risks of being an inadequately-armed vampire hunter). Over the course of the game, he meets several characters who know all about it. Those characters being Eric Lecarde and his daughters.
Dragon Age: Origins loves this trope. All of the Grey Wardens, including Duncan and Alistair, keep everybody locked out of the loop regarding the risks of joining their order and indeed why they're necessary, fearing that no one would become a Grey Warden if they knew. Morrigan keeps you locked out of the loop regarding why she joined your quest until almost the end of the game. Zathrian really, really isn't telling you the whole story about those werewolves. And so forth.
Yuki from The King of Fighters was like this at first, in regards to her boyfriend Kyo's double life as an Ordinary Highschool Student and a street fighter. In the tie-in manga "KOF: KYO" she learns about it and isn't happy, but forgives him. (It doesn't help that she only learned about it when Athena transferred to this school and then Iori Yagami showed up.) However, she remains outta the loop in whart concerns her heritage and destiny in the whole Orochi story... as the as-of-now last descendant of Princess Kushinada, the legendary Barrier Maiden that must be ritually sacrificed so Orochi will return to this world. When she's kidnapped for that and then rescued, Kyo and others keep the reason behind it outta her knowledge.
In Tales of the Abyss this trope is somewhat exaggerated: from the start of the game, every single party member except one has a different part of the loop that they're keeping the main character locked out of, for their own reasons, and for the most part unaware of all the others. Guy has been plotting with Van for years to kill Luke in front of his father as revenge for his own family's death. Anise is secretly reporting on all of their actions to Grand Maestro Mohs because he has her parents hostage. Tear wants to kill her brother because he actually wants to destroy the world, but she doesn't think anyone will believe her if she just says so because he's a Villain with Good Publicity. Jade figures out that Luke is a replica about two scenes after you meet him, but doesn't want to deal with the hassle of explaining when it's not relevant to the mission. The only one not deliberately keeping secrets from him is Natalia, and that's only because she doesn't know her own secret.
Angie in Shikkoku No Sharnoth thinks that Mary has become the mistress of a rich man out of despair at her friend Charlie's condition. She's wrong, of course, but Mary only clears up the misunderstanding without actually explaining what she is doing.
Tsukihime: Honestly, does anyone tell Shiki the stuff he really needs to know? The only one who's really honest with him, Arcueid, doesn't actually know a thing about his backstory. Even the other sane love interest never feels that it's necessary to tell him or flat out lies about the twin switch so Kohaku doesn't realize he simply mixed them up until far too late.
In Little Busters, Riki and Rin are the only ones in the main cast who don't know the secret of the world - that this world is a fake created after a bus crash left all but Riki and Rin near death. Why he's locked out varies - Kengo just wanted to be able to live happily in this world forever without worrying them about reality, while Kyousuke was deliberately trying to build them up and make them stronger so when they went back to the real world they could function on their own.
Antimony in Gunnerkrigg Court was rather shocked to discover some facts about herself and her mother while all Surma's friends knew. And then it turns out this wasn't the only secret and this was even more widely known... "Seems like people enjoy keeping things from Annie" indeed.
Off-White: Iki doesn't know he's a white spirit. Raigho started to tell him, but was interrupted.
Dan and Mab's Furry Adventures : Dan's an incubus. His mother was one of the most powerful and infamous 'Cubi around. No one told Dan this until his 'Cubi heritage started manifesting itself. His (non-cubi) half-sister, Alexi, didn't think he'd take so long to ask.
Homestuck: The other characters deliberately avoided telling John that Vriska had died because they knew it would upset him.
Everyone except for the main characters in L's Empire seem to know the significance of Beware the night of five lights. Since Dark Star is a god, he's able to know anything that has happened on screen. If the main characters found out, he would find out.
In Worm, Crucible, a new member of the Brockton Bay Wards, is completely unaware of the circumstances of Cauldron's presence in the PRT and Protectorate due to having joined after the events of Echidna. His teammates regularly bait him about this.
Crucible: Again with the Echidna thing. Can't you tell— Clockblocker, Kid Win, and Vista [in chorus, with Kid Win not even looking up]: Classified. Crucible: Fuck you guys.
Winx Club: In the first season, Bloom does not know she is the princess of a dead planet, and the guardian of a special power called the Dragon Fire. That is, until the Trix, who do know, take it away from her.
It is painfully obvious to everyone that Dale's son Joseph on King of the Hill is actually John Redcorn's lovechild. Everyone, that is, except Dale, and no one tells him because... well, because he's crazy enough already. When he does figure out that Joseph is not his son, he immediately concludes that Nancy was impregnated by aliens, and everyone leaves it at that. The irony, of course, is that Dale mistrusts EVERYONE and accuses everyone ELSE of trying to backstab him... Except John Redhorn.
In Avatar: The Last Airbender , the Earth King Kuei is being kept in the dark by his "cultural authority" the Dai Li as to the fact that there's been a hundred-year war between the Earth Kingdom and the Fire Nation. The Dai Li is mostly engaging in this to maintain power and to "prevent chaos." They also maintain an oppressive control over the city itself; people who disrupt the city or talk about the war are either terrified into silence or hauled off for "reeducation" into Dai Li sleeper agents.
In the Futurama episode "Parasites Lost", the crew has to make sure Fry doesn't know their plans to rid him of the worms. If he finds out, the worms will know too and can mount a defense.
In the Men In Black episode, The Out to Pasture Syndrome, Zed decides to retire. When Alpha returns more powerful than ever, he captures J and uses a Mind Probe to discover Zed's location. After he leaves, Agent L rescues J and reveals Zed's not retired: every last one of J's fellow agents had kept him out of the loop so that Alpha would read J's mind and believe the lie, so they could ambush him. Unfortunately, J was confused as to why Zed's eyes didn't glaze over when he was neuralized, and Alpha picked up on that.
Through the first four seasons of The Venture Bros., Hank and Dean didn't know they were clones. Dean finds out in the interlude Halloween episode between seasons 4 and 5, but chooses not to tell Hank.
This really backfired early on in W.I.T.C.H.. The girls learn that Elyon's a princess and that her brother, Big Bad Prince Phobos, is looking for her. Cornelia's all for letting her know right away, but Will isn't so sure of doing so. Then, she finds out from Phobos and Cedric, leading to Elyon believing all of their lies and running off with them. Corny isn't too happy with that bit.
Adopted children sometimes don't know they were adopted until they become adults. Sometimes, they never find out.
In the first half of the 20th century, quite a few U.S. doctors considered it most merciful to tell a terminally-ill patient that they were sure to recover soon, but clue in the family to the real state of affairs.
Notably, the Catholic Church's reaction to this notion was What the Hell, Hero? on account of viewing not telling the patient that he is not long for this world as cruelty disguised as mercy, as it denies the patient time he could use to make his peace with God.
Even today, many doctors believe it is best to keep a woman from knowing if something is wrong with her unborn child—as stress increases the likelihood of something going wrong with unborn children.
Pakistan was locked out of the loop while the US conducted an operation to kill Osama bin Laden. The operation succeeded in 40 minutes, and Pakistan was only informed a couple hours later. This has been happening on a more general basis in US Pakistan relations, for the simple reason that things the US told them kept getting leaked.
Intelligence agencies that normally cooperate (such as the American and British agencies) will start keeping things closer to their chests if they think their ally has a mole or a leak.
In politics, aides, advisors, and operatives often take actions without telling their boss— precisely so that if the situation does blow up in their faces, they can (truthfully) claim that they'd acted alone and their boss didn't know. This is called "plausible deniability". (The word is often misused to refer to a politician who did know but pretends not to.)
Can also lead to politicians not monitoring certain of their aides, advisors, and operatives too closely so that if they are doing anything improper and keeping it from them, they won't accidentally find out.