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Amnesia Missed a Spot

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Uh-oh. The Masquerade that you've worked so hard to build and maintain has suddenly been broken. Now a bunch of Muggles know that you and your entire family are vampires/werewolves/witches/what-have-you. But no problem. All you've got to do is whip up some mojo and give them a handy case of Laser-Guided Amnesia, right?
Well, no. See, turns out your spell/hypnosis/whatever, didn't work the way you'd intended. Sure, maybe it wiped the memory of a few, but there was this one guy whose memory remained intact. (Probably The Hero or someone close to them, but most certainly a character who has relevance to the plot. This trope is not wasted on minor characters.) For another a variation, the character in question may have their memory mostly wiped, but retain some crucial piece of information relating to The Masquerade. (Which they may not immediately recognize the significance of.)
Fake Memories usually have similar problems, someone always finds the holes.
The "partial erasure" version can result in a "I Know You're in There Somewhere" Fight attempt by a friend who tries to get the amnesiac to remember.
Compare Ripple-Effect-Proof Memory (which may overlap) and Glamour Failure. Contrast Laser-Guided Amnesia, which is when the mojo works. Wistful Amnesia is a subtrope where a weaker version of this effect (that is, the victims don't remember more than that they've forgotten something) is directly caused by The Power of Love or The Power of Friendship. Amnesiac Lover can overlap with this trope if the "spot" was someone in a relationship with one of the victims. Amnesiac Dissonance (which is when skills that the amnesia allegedly should have erased come roaring back) also has overlap.
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Fear and Loathing in Las Vegas gives us a non-magical instance; Duke mentions how some people who have a bad trip on LSD have trouble remembering anything save for a few scattered details. He mentions this in reference to the girl his attorney effectively drugged and kidnapped, Lucy, stating that even if they just set her loose and hoped her memory was fucked, she might "spend two more days in the grip of total amnesia, then snap out of it with no memory of anything but our room number at the Flamingo [Hotel]."
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Finding Nemo: When Dory is swimming around the chain in the Sydney harbor, having lost grip on her memories again, she remembers almost nothing except that she "lost someone". She could either be referring to Nemo, who she has been watching Marlin frantically track down for the last few days, or Marlin himself, who has just left her behind - the reason she's now lost and confused in the first place. The memories return when she hears the name "Sydney", which she has been repeating to herself the whole movie. A bit of a different example, since Dory has a fairly accurate case of real-life anterograde amnesia; her memories simply fell apart because she lost the social connection she associates with them. The Sydney address, another connection she has to her friend, repairs them.
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In Matched by Ally Condie, witnesses to an event are ordered to take a mind-wiping pill, but the main character only pretends to and keeps her memory.
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Bleach:
When Soul Society takes Rukia back, they mind wipe everyone and leave no traces of her existence behind. The only people unaffected are those who possess a significant amount of reiatsu: Ichigo, Chad, and Orihime.
In Fade to Black, the antagonists possess a scythe that can erase the memories of anyone it cuts, as well as everyone's memory of that person. Ichigo is able to recover immediately due to his powers having been awakened by Rukia, and Kon is completely unaffected (possibly by virtue of being an artificial soul).
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Because I Knew You opens with Wanda Maximoff sensing the spell to erase all knowledge of Peter Parker, allowing her to use her powers to protect herself from what she believed was an explicit attack on her before she learned that it was actually a worldwide effect.
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RoboCop (1987): After his transformation into RoboCop, what remains of Officer Murphy's mind experiences flashbacks of his prior life despite his memory being wiped.
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The Chronicles of Prydain novel The High King. Arawn Deathlord created the Cauldron-Born by putting dead bodies inside his Black Cauldron. They are mindless zombies completely under Arawn's control with no memories of their previous lives. When the defenses of Caer Dathyl were breached and the Cauldron-Born prepared to enter they saw King Math standing before them.
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In The Girl from the Miracles District, the Order had Robin's memories wiped out prior to the beginning of the story, but Robin retains a few scattered memories. Subverted as they're fake memories implanted specifically so that he wouldn't question his supposed backstory. There're also the Recurring Dreams which are the real missed spot in his memory wipe.
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In another post-No Way Home example, Spider-Man: Finding Home sees Peter forced to answer Shuri's questions regarding the complete lack of information about him when Spider-Man becomes a suspect in the murder of General Okoye. When a blood sample confirms that Peter is related to Richard and Mary Parker, Shuri's subsequent search of electronic records shows no direct sign of Peter's existence in the remaining records on Richard, Mary, Ben and May, but Shuri is able to find an anomaly in Ben and May's tax records that indicates they either used to have a dependent claim that has since been erased or they were committing serious tax evasion for years.
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The Castle fic Florida Heat opens with Kate Beckett being found in a hospital in a battered condition with amnesia. The first memory she regains is a memory of walking past a group of paparazzi who greet her as "Nikki Heat", and while the doctors obviously assume she's confusing herself with a fictional character, she subsequently recognises a photo of Castle and convinces them to call his publishers to get his number.
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 Castle (2009)
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In The Power of Seven, after Harry is trapped in a fake reality where he never went to Hogwarts, he retains enough memory of his real life that he knows Ginny's name when she manages to make contact with him even though he's never met her in his current memory. He starts to show more recollections after Hermione and Luna come to him, although he still consciously remembers relatively little of his true life until his encounter with Demelza restores his sense of control.
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In Doctor in the Underworld, as far as Erika is concerned, she has spent the last sixty years as a servant to the vampire coven since she was turned, allegedly because she was dying of consumption in a German cabaret, and has no memory of her life before that. However, she swiftly recognises the Tenth Doctor's scent once she's in the same room as him, even though the Doctor was hiding and she last smelled him when she was human over two centuries ago, and also immediately feels an attraction to him when they come face to face.
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In Genocide Man Joey reveals that his tweaked augments make him immune to the Lethe Protocol they use for discussions of things so terrible that plausible deniability isn't enough. He takes advantage of that immunity to jog Jacob's memory of voting to use the Guyaquil Complex that killed a billion people.
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Jack in Oblivion (2013) has dreams of New York before the Scav invasion, despite his memory wipe to maintain secrecy. It's actually Genetic Memory, he's a clone.
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Some of the girls from The World God Only Knows remember stuff after Elsie erases their memories. They usually come up with their own version of what happened to explain. This is explicitly because New Hell has power issues, and only erases the absolute minimum. This can bite Keima in the ass; for example, he took a girl to an amusement park for a date, which ended in a kiss. According to her memories, he ditched her halfway through for no reason whatsoever.
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The memory drug in Torchwood, called "Retcon", can sometimes leave nagging little details in the victim's mind. If they're distanced from all the weird things they've seen, it won't be a problem, but if something triggers it the memories come back. This is how Gwen re-learns of Torchwood in the pilot after Jack wipes her mind.
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In X-Men: Evolution, an entire sports stadium of people learn about the different mutants among them and their powers. To maintain their secret identities, Professor X tries to erase everyone's memory of the night, but blacks out before he can finish erasing Principal Kelly's mind. Principal Kelly later goes on to be very anti-mutant.
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X-Men: First Class: At the end, Xavier wipes MacTaggert's memory to keep the mutants safe from the CIA. All MacTaggert remembers is a few glimpses of leaves and Xavier kissing her.
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In Persona 2, at the end of Innocent Sin, Philemon recreates the world at the catch that everyone will forget everything that happened in the game. Tatsuya Suou, The Hero of Innocent Sin, keeps his memories out of sheer willpower, but is forced to give them up at the end of Eternal Punishment. Big Bad Nyarlathotep, of course, remembers everything due to his supernatural status and restored the memories of the Ax-Crazy Pyromaniac Tatsuya Sudou.
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In Persona 3:
Ordinary people who don't experience the Dark Hour have their memories revised afterwards to explain anything strange that occurs during the Dark Hour. (Which they might notice after it passes). In one scene, Mitsuru mentions that so many people are coming down with Apathy Syndrome that the memory revision can't keep up.
At the end of the game, either the protagonists (in the bad ending) or the entire world and the protagonists (in the good ending) have their experiences of the Dark Hour, as well as all the bonds of friendship and Character Development that occurred because of it, erased from their memories. Everyone, that is, except for Aigis, who explicitly remembers everything. Depending on which ending it is, the character's situation is either wistful or downright Fridge Horror, because in the bad ending she knows that The End of the World as We Know It is hours away from happening but there's absolutely nothing she can do to stop it, and she can't even tell her former friends about it because they don't even remember who she is.
It's also implied to have missed to the Main Character in the good ending, since he/she can speak to Aigis about it in the last two days before graduation. However, since the narrative skips from the aftermath of the Final Battle to the day before graduation, it's ambiguous whether he/she retained all memories along with Aigis and simply kept quiet about it for three months, or whether the memories came back on that specific day.
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Men in Black:
Men in Black: When J meets Dr. Weaver in the Morgue, they vaguely notice that they may have met before, but dismiss it as Deja Vu. In the beginning of the movie, they had met, but K had wiped both of their memories of an apparent alien encounter. It's mentioned previously that a neuralizer leaves one feeling a vague sense of deja vu.
Men in Black II: Kay neuralyzed his own memories about his run in with Serleena and Lauranna, but watching the "reenactment" causes some of the memories to come to the fore.
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In Throw Away Your Mask, Akechi regains his wiped memories of the Dark Hour very quickly due to how laser-guided the Laser-Guided Amnesia was: he still remembers his time-travel, and it's not hard to figure out something is amiss from there.
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In RahXephon, the Mulian mind control is shown to be imperfect when Hiroko realizes she has forgotten something really important when she meets Ayato again after his disappearance.
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Discussed in the Marvel Cinematic Universe fic Tingle; post-Spider-Man: No Way Home, after Peter starts dating Kate Bishop and Yelena Belova, when he first explains about the memory wipe, Kate asks if she had met him before the wipe considering how quickly they bonded, but Peter assures her that the first meeting she remembers was his first meeting with her as well.
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An Iron Man arc made it pretty literal: Tony Stark fired up a virus that erased all information of him from the Internet and memories from everybody around the world... and then it turned out that Doctor Doom still remembered. The amnesia virus was not able to make him forget that he had written a diary by hand (so it could not be hacked for deletion) that mentioned Stark.
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In the Stargate SG-1 fic I Will Remember You Part 4- Fallen, after Daniel's return to human form cost him all memory of his time Ascended, he eventually realises that he was able to 'protect' his own memories of his romantic liaison with Sam during his Ascension, regaining those memories after he and Sam have sex while he's human for the first time.
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You Were My Best Friend: When Bloom turns seven, her dance teacher, Madame Morgana, suddenly disappears and everyone else forgets the woman existed in the first place. Everyone but Bloom. Seeing Bloom is actually a fairy from another dimension, it makes sense she'd remember.
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Danganronpa: Trigger Happy Havoc:
When he gets sick with a high fever in Chapter 5, Makoto remembers that he should want to stay in the school, rather than escape it. He doesn't quite understand the context or the ramifications of this until the final Class Trial.
Kyoko reveals that she can't actually remember what her Ultimate talent is, but she remembers enough that she knows the Mastermind has tampered with her memories.
In the final chapter, at one point of the investigation, Toko ends up inadvertently seeing a severely impaled corpse, causing her to faint and wake up as Genocide Jill, who reveals her memories are different to that of Toko. During the final trial, this detail is brought up with it being revealed that when the Mastermind erased two year’s worth of memories for the cast, they failed to account for this, and as such, Genocide Jill actually remembers what happened in the backstory, including the ruined state of the outside world.
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In Super Powereds, this is done deliberately to Nick, on the condition that he pass a Secret Test of Character.
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Invoked in Eternal Sunshine of the Spotless Mind: the Laser-Guided Amnesia works by destroying the connections in the brain that are attached to the stored memories to be removed, causing the memories to fade away. When Joel changes his mind about having his memories of Clementine erased during the procedure, he tries to hide his memories of her within other memories where they don't logically belong. Unfortunately, the doctor performing the procedure is able to tell when he goes off the "map" and force him back onto it. However, in the end Joel remembers just enough of Clementine that he is able to find her again and they start their relationship anew.
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Twice on No Ordinary Family with the same characters.
Daphne uses her newfound idea push powers to tell her inquisitive boyfriend not to ask about the family's special abilities. It works, but then a few hours later he broaches the topic again. So she pushes again, which works for a few hours again. Etc. She finally ends up telling him.
Jim convinces Daphne to mind-wipe BF of his knowing about the family, so she gives him the instruction to "forget about when you learned I was special." This time it works too well, as he forgets their entire relationship.
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In the Animorphs series A Splash of Blue, the key divergence from canon is that Loren is still a part of Tobias's life. While the Ellimist has erased all conscious memory of her life with Elfangor, she still expresses some vague recollection of those events that she expresses through her artwork; once the Animorphs know what to look for, they can see how some of her paintings that appear to be splashes of blue are actually a representation of an Andalite (although they don't initially realise it's Elfangor), and Cassie even notices how an image of a Taxxon shows a sense of sadness, suggesting that it represents Arbon in particular. When the Animorphs rescue Ax from the dome, Loren immediately "recognises" him as 'Al' and talks about how she thought he couldn't look like that any more, even if nobody else knows that she is recalling Elfangor himself.
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In Aveyond 2: Ean's Quest, the Snow Queen kidnaps Iya so that she can use her as a Human Sacrifice to freeze the world. To ensure that no one will oppose her plans, she makes the citizens of Elfwood forget about Iya. Only Ean, her Childhood Friend, remembers her and sets out to rescue her.
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A few examples in Yamada-kun and the Seven Witches:
Because Tamaki is a witch-killer, he's one of only a selected few people who can remember Yamada after Rika's memory wipe. He can also remember Yamada after Ushio's memory wipe, but he's not a witch-killer anymore by this point, and it's never explained why his memory is retained.
Because the seventh witch power doesn't reach people who are not physically present at Suzaku High, Leona is another of the selected few people who can remember Yamada after Rika's memory wipe. She can also remember him after Ushio's memory wipe because she, along with the other third-year students, are at home studying for her exams that day.
Because Takuma's anemia forces him to stay at home on election day, he's yet another rare person who can remember Yamada after Ushio's memory wipe.
The chairperson is immune to having her memory wiped by the seventh witch power, though it's never explained why, only mentioned that it probably has something to do with her status as the "Akashic recorder".
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In one episode of Futurama it looks like Fry was ground up into sausages and Leela goes to a memory erasure clinic to relieve the pain of his death. She is told before the procedure starts that it only hides memories, it doesn't remove them entirely and she might accidentally remember again. Meanwhile Fry is actually living among a Neanderthal tribe with blunt trauma-induced amnesia. Naturally, they both regain their memories upon meeting one another again.
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In Code Geass, after having her memory wiped in the first season, Shirley finds a crumpled up letter that she had dropped beside her desk that tells her Lelouch is Zero. Then in the second season, she gets memory wiped again, but eventually regains her full memories after being accidentally hit by Jeremiah Gottwald's new Geass Canceler, which undoes the effects of both memory wipes.
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In Fantastic Beasts and Where to Find Them, Jacob Kowalski has to have his memory erased after the climax in accordance with magical law, but at the end he's shown to have made pastry replicas of various magical creatures, without knowing where he got the ideas from. He also seems to remember Queenie when she visits him. As explained in Fantastic Beasts: The Crimes of Grindelwald, he didn't have his memory fully erased at all; the erasure only removed his bad memories of magic, but he didn't consider most of the memories bad. He was apparently just lying about not knowing where the magical beast ideas came from.
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In What If?, Thalia Reagan consciously remembers nothing of Trinity’s life, but she experiences a recurring nightmare of watching Neo ‘die’ when Cypher pulls the plug and swiftly finds herself aware of what to do once she starts hacking again despite having no conscious memory of Trinity’s skills; Lloyd himself experiences a few dreams of Cypher watching Trinity, but never realises their significance.
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Fallout: Equestria - Project Horizons: Jetstream was so distraught by her lover Stonewing's death that she asked Vanity to remove the memories of him as she was going insane with grief. Vanity reluctantly agreed, but this only led to Jetstream's mental breakdown when their friend Big Macintosh dies. This triggers her to remember Stonewing and the realization of her lover and best friend's death drove her permanently insane.
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The protagonist of Paycheck has glimpses of what he was supposed to forget, along with the envelope full of notes, apparently because his last job used chemicals instead of the usual neuron-zapping, which is apparently complete.
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In The Heroes of Olympus, Percy's memories of the events of the previous series are almost completely wiped at the beginning of The Son of Neptune. The "almost" is his memory of his girlfriend, Annabeth, though it's dim. Just knowing her name motivates him to keep fighting and gradually regain his other memories.
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The Spider-Man storyline One More Day ended with basically the entire world forgetting that Spider-Man's true identity was Peter Parker (as well as Peter himself forgetting his marriage to Mary Jane). Discounting Peter and Mary Jane, until Peter unintentionally weakened the spell during Spider-Island, the only people shown to still remember Spider-Man's identity without him revealing it to them were Kaine (Peter's clone), Miles Warren/the Jackal (the man who created Spider-Man's clones) and the Hulk (from Hulk's description, the spell only erased the memory of the personality that was in control when it was cast, with the others remembering after they transformed).
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The "Not-Them" from The Magnus Archives are creatures who murder people and seemingly rewrite reality to take their place even though once they are finished, though they look human they don't resemble the person they replaced in any way. In every story featuring them, there is always a single person who knows they are not the real person (so far, someone who didn't know the person very well or was estranged from them). However, since said person is then taunted and tormented by the Not-Them, it's implied that they miss said people on purpose.
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A character in an optional side quest in Deus Ex: Human Revolution had augmentations installed to keep him from remembering certain missions. However, fragments remained, which let him to knowing that his mind was being tampered without his consent or knowledge.
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Fairy Tail: In the Tenrou Island arc, Magic Council Agent Doranbolt altered the memories of the Fairy Tail guild to not only make them think that he was a member, but that he was was also Mystogan's apprentice and an S-Class candidate for the upcoming exam. The one being he failed to target was Pantherlily, Mystogan's companion from their home dimension of Edolas, who knew that Mystogan's secret quest to find the Animas meant he couldn't take on an apprentice.
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In the Danny Phantom episode "King Tuck", Tucker uses the scepter to make everyone forget the events of the episode save for himself and his two friends. Unfortunately Star and Paulina mishear "hand-made in Japan" as "handmaiden" which they were forced to serve as during the adventure. For reasons they can no longer remember, this drives them into a furious rage, and they quickly give chase.
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Digital Devil Saga. Many people, NPCS and playable characters, mention that they are recalling events that they know they have not experienced. Many others note that they have knowledge of things that do not exist in the world they live in. This happens because everyone is the reincarnation of someone who died in the real world.
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The Magicians reveals that those who fail the highly-demanding entrance exam to Brakebills have their memories of the experience erased, before being given a suitable alibi for their absences and sent on their way. However, Quentin's friend Julia proves just resistant enough to figure out what happened and even begin a few rudimentary magical studies of her own, eventually forming the basis of her chapters in the second book of the series, The Magician King.
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Men in Black II: Kay neuralyzed his own memories about his run in with Serleena and Lauranna, but watching the "reenactment" causes some of the memories to come to the fore.
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Quantum Devil Saga: Avatar Tuner:
While Sera remembers nothing about herself, she still remembers everything about all sorts of subjects such as literature, science, mythology and daily life facts.
Lupa has no memories from his previous life but he has kept all his combat abilities and behavioral patterns, and admits to feeling very familiar with the people he was previously acquainted with.
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Doctor Who: In "The End of Time", Donna Noble, who received Victory-Guided Amnesia in her previous appearance in order to prevent My Skull Runneth Over, gives her grandfather Wilf a book by billionaire Joshua Naismith, who is connected to the events the Doctor is investigating (the book allows the Doctor, who had been shown Naismith and his daughter in a vision, to learn his identity). She has no idea why she felt the book would be a good gift, and the Doctor speculates that her suppressed Doctor-Donna side is still fighting for them even now.
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Men in Black: When J meets Dr. Weaver in the Morgue, they vaguely notice that they may have met before, but dismiss it as Deja Vu. In the beginning of the movie, they had met, but K had wiped both of their memories of an apparent alien encounter. It's mentioned previously that a neuralizer leaves one feeling a vague sense of deja vu.
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In Fade to Black, the antagonists possess a scythe that can erase the memories of anyone it cuts, as well as everyone's memory of that person. Ichigo is able to recover immediately due to his powers having been awakened by Rukia, and Kon is completely unaffected (possibly by virtue of being an artificial soul).
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In the Biker Mice from Mars fic Evil Jack: Domestic Bliss, Jack McCyber and Karbunkle have worked together to wipe Charley's memory of her life with the Biker Mice and even create a genetically-engineered daughter for her and Jack to reinforce the deception. Despite Jack's cover story of trauma-induced amnesia, Charley quickly feels too many anomalies in her life with Jack and retraces her steps to reunite with the Mice, even if she swiftly acts to protect Hannah despite finding evidence that she's never been pregnant.
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In the Empath: The Luckiest Smurf novel, the Psyche Master claims to have completely erased all of Empath's memories as an infant so that he would have no memory of ever being Papa Smurf's only biological son. However, the erasure procedure left only that memory of the infant Empath crying when he saw his father leave him in Psychelia just moments before the procedure started.
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Safehold: The original colonists of the planet, the "Adams and Eves", had their original memories erased, which was part of Operation Ark's original plan, and were programmed to believe in the administration's God Guise, which wasn't. In book 8, Hell's Foundations Quiver, it's revealed that folklore hero Seijin Kohdy was real, and that after former Sergeant Major Cody Cortazar had his old combat skills reactivated to turn him into a seijin to fight in the war against the faction who disagreed with the administration posing as "archangels", he began to remember things he wasn't supposed to, such as his first language, Spanish. He was murdered and unpersoned when he tried to talk to the "archangels" about this, but an Ancient Tradition survived, keeping his journal.
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Glitch Techs: Or, in Miko case, "Amnesia Missed Entirely". Miko is completely immune to memory wipes. Even when Hinobi's memory-wiping devices are turned up to the highest-possible percentage that would induce total memory loss, all that returns is an error message. The show was cancelled before it was ever explained why this was the case.
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In Path of the King when it becomes necessary to make Detective Dojima forget about the events related to Guilford's mansion, Tohsaka does an impressively good job of manipulating his memories via hypnosisnote (Her spot checks include using his trance to press him for info on possible conspirators or incriminating records that would jog his memory). However, he still notices that something is amiss because the reading of his car's odometer indicates about 50 kilometers more than the expected number.
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In Travelers, several people close to the main team are kidnapped and told about the Traveler program. Eventually they all get their memories of the event erased, but one of them is an alcoholic whose tolerance gives him some resistance to the mind-wipe drug, so he starts to remember things and cause trouble for the team. Another one remembers having similarly lost a day earlier in the show, which leads her to start becoming suspicious and even afraid of her "husband".
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In The Wotch, four Jerk Jock football players are transformed into much nicer cheerleaders. They don't appear to remember their past selves beyond vague notions of some jerks harassing Wolfie. Except, as revealed in Cheer!, its spinoff, Jo actually does remember, but is keeping it to herself.
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In the Stargate Atlantis fic Orpheus, John Sheppard and Elizabeth Weir accidentally activate a device intended to erase a person from the memories of all who knew them. The inventor’s purpose in creating that device was to help people move on from the pain of a death by erasing all memory of the deceased, but Elizabeth is accidentally erased by the system while still alive, leaving her briefly trapped in another dimension. Fortunately John Sheppard retains his memory of her (suggested to be because his feelings for her are so strong they resisted the memory-wipe) and is able to reverse it.
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Star Wars Legends: Knights of the Old Republic has this as the backbone of the plot. Revan's fragmented memories, as spied on through Bastila via the Force Bond were supposed to lead the Jedi to the Star Forge with your Player Character being none the wiser.
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Played with on House of Anubis, When Fabian gets his amnesia curse. At first, he is still able to remember enough, like who Nina is, even though it does take a little work to trigger these memories. Though, eventually he does lose his entire memory, including his name.
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Mind-wiping in Artemis Fowl leaves "residual memories" which can be used to trigger total recall.
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The ending of Crisis on Infinite Earths shows that only the Psycho-Pirate remembers the multiverse or the details of the Crisis itself. Everyone else only has vague memories of a big battle and the skies turning red. He apparently attempted to inform people of what actually happened, only for people to assume he's insane, so they sent him to a mental institute.
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In Fullmetal Alchemist, Greed seems to have been completely mind-wiped... until he comes across and kills one of his last surviving friends from before the mindwipe and abruptly collapses under the subliminal My God, What Have I Done? There's even an in-universe explanation: Greed's friends are part of his soul, and therefore can't be erased from him, even if he forgets them.
 Amnesia Missed a Spot / int_f70c0e06
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 Amnesia Missed a Spot / int_f70c0e06
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 Fullmetal Alchemist (Manga)
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Amnesia Missed a Spot / int_f70c0e06

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