Static: Mr. Hawkins, I'm glad to see you're okay. Mr. Hawkins: You can drop the act, Virgil. Static: You know? Mr. Hawkins: Wasn't hard to figure out. Why else kidnap me to get to Static? And maybe, maybe in the back of my mind, I've always known.
We all know about Secret Keepers: One or two people that The Hero trusts enough to tell about his superpowers. However, there are also "secret" Secret Keepers who figured out the character's secret on their own, and instead of confronting the hero about the secret, decide to keep things quiet. They then almost always take it upon themselves to help the hero secretly from the sidelines by creating distractions to allow the character to slip away to change unnoticed, letting the hero know about dangers or problems that need the hero's attention, and so on.
If a reason why they don't just tell the hero, "I know," is given, it's usually pretty flimsy.
Sub-Trope of Secret Keeper. See Also: I Know You Know I Know and Keeping Secrets Sucks. Everybody Knew Already is when everyone is this. Locked Out of the Loop is what those who are openly (so to speak) in on the secret assume of this character, which may lead to a twist, depending on whether the audience knows they know.
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An occult otaku character in the Vampire Princess Miyu TV series is an asymmetric Secret Keeper. However, at the end of the first episode, he confronts Miyu, and she frightens and deceives him into walking off a roof to his death, because he asked her to make him a vampire and started going on about being above the normal people — Miyu found this an offensive misunderstanding of the role of vampires in the setting — both making him Sacrificial Lamb to further establish the series' dark tone, and helping to establish Miyu's role as a Dark Magical Girl in the early series.
In Tokyo Mew Mew, Ichigo worries on a regular basis about people discovering her secret, and on many an occasion, her worry works her up enough to almost let it slip. However, Aoyama Masaya, the one person that she wanted never to find out because she was sure he'd reject her, figured out her identity on his own and is perfectly fine with it. This is the point where they become without a doubt an Official Couple. Unknown to the both of them, he has some not-quite-normal qualities himself.
Honoka's grandmother, Sanae, in Futari wa Pretty Cure. It's unclear just how much of the secret she knows, though. She seems to enjoy being mysterious about it.
Euphemia for Lelouch in Code Geass; at least, for a little while. She's the first person to figure out Zero's true identity, but keeps this to herself until the two are able to meet privately.
Shirley is briefly this after she finds her note to herself from before Lelouch erased her memory, and then again when Jeremiah inadvertently deactivates Charles' Geass on her.
There are several of those in Sakura Gari, and they all guard extremely creepy secrets:
Sakurako, as a child, witnessed Katsuragi and Souma killed her mother, whom everyone thought she committed suicide
Souma found out that Sakurako killed his ex-lover Terashima
The old maid and Katsuragi know that Sakurako's mother abused Souma.
Near the end of Sailor Moon R, it is heavily implied that Usagi's friend Naru had figured out Sailor Moon's secret identity on her own when she tells Usagi to be careful before confronting the season's Big Bad. However, they never actually confirm this directly, and then appear to retcon this bit of character development in future seasons. A couple of other single episode only characters figure it out: Asai Tsutomu, an old friend of Minako's who figured out she was Sailor Venus when he saw Venus use Minako's special volleyball move and did hint at least he knew to her, and Saori who had a crush on Mamoru till she overheard him call Sailor Moon "Usako" and gave up on him without explaining why.
During the Desperate Revival arc of Detective Conan, Ran had figured out Conan was Shinichi, but didn't confront him about it because she was waiting for him to tell her. As you would expect, she's thrown off once again by the end of the arc and no longer has this role.
In Tiger & Bunny, Vigilante Man Lunatic/Justice Yuri Petrov knows Wild Tiger/Kotetsu T. Kaburagi's secret identity and decides to keep it to himself. Despite the antagonistic relationship between them, this actually works out for Kotetsu, as Maverickdoesn't mindwipe Yuri like he does most of Kotetsu's other Secret Keepers when he Unpersons the hero. It isn't made clear as to whether or not he is able to discover Kotetsu's identity himself, or if he simply has access to the information due to his aforementioned position.
For the first few episodes of Sonic X, Chris and his Grandfather were this for the Sonic characters. Then came just one subversion after another as Tanaka the butler reveals he worked it out ages ago, Chris TRIED to tell his mother but she is quite frankly being mind numbingly clueless about it and they realize that they're upsetting the cleaner so much by trying to keep it quiet that they let her in on the secret - and she ends up fussing enormously over Cream and playing a substitute mother figure.
In Pretty Sammy, it turns out her whole class knew Sasami was Pretty Sammy and were just being polite about not letting on.
Sugi of Girl Friends is the first, and probably only, one to figure out Mari and Akko's Secret Relationship. She occasionally teases them subtly about it, making them worry about how much she knows, and in the last chapter helps the two have some alone time together, after being surprised that she's still the only one amongst their circle of friends who figured out that the two are a couple.
In Mahou Sensei Negima!, Negi trains with Kaede in the mountains for the day. He departs the next morning, thinking that Kaede is still asleep, unaware that she's watching (in his defense, though, with Kaede it can be hard to tell). She shrugs it off and later shows up in Kyoto when Yue calls for help. After the incident is resolved, Negi explains things to her and the others. We never find out if Kaede mentioned that she already knew.
Suzie Wong of Digimon Tamers is one. As soon as Henry shows that Terriermon is alive, she admits that she knew it all along.
In Bleach, it turns out that Isshin knew Ichigo was a Soul Reaper the whole time because he's actually a former Soul Reaper himself.
Dengeki Daisy is an interesting case, due to the fact that the Secret Secret Keeper is the exact person that the secret is supposed to be kept from in the first place.
In Fairy Tail, it's revealed that Bickslow knew all along that Loke was really a Celestial Spirit, thanks to his Aura Vision.
In Pre CrisisSuperboy, Pete Ross is one for Clark Kent'. Later, his son discovers Superman's secret identity and, not knowing his father knows, doesn't discuss it with him.
Iris West, the wife of the second Flash, for a year after they got married (it turned out he talked in his sleep...); she didn't mention it because it seemed so important to him that it be a secret.
Ashley Zolomon becomes this for Wally West, the third Flash, after a Cosmic Retcon that caused everyone to forget his secret identity (previously it had been openly known, before that knowledge caused his wife Linda to be attacked). This gains special significance because Ashley's estranged husband-turned-supervillain was the one who attacked Linda in the first place.
What makes the above example interesting is that the character doesn't put two and two together on their own. To whit: during the Rogue War storyline, Zoom (Ashley's ex-hubby) speeds her to Wally's house, the one place he knows she'll be safe during the titular citywide clash, while declaring to her that Linda (who's there at the time) is the Flash's wife. Later, at the end of the story, Ashley's writing up a profile on the Flash, pauses when she gets to the section about the hero's real name, then deliberately writes "Unknown." Hence, she knows Wally is the Flash, and Linda knows that Ashley knows—but neither of them tells Wally himself.
In Spider-Man, both Mary Jane and Aunt May were eventually revealed to have been secret secret keepers for years (with Aunt May largely in denial), though this was not known to the reader. Aunt May let Peter know the truth shortly before she died during The Clone Saga ("Peter, what is it like to fly?") Then it turned out that was a "genetically-altered actress"...
Captain George Stacy was this for Spidey as well. When he was mortally wounded during a fight between the web-slinger and Dr. Octopus, he revealed his knowledge of Peter's dual identity even as he died in the hero's arms.
In Ultimate Spider-Man, bully and Flash Thompson's friend Kenny "Kong" McFarlane was convinced Peter Parker was Spider-Man when his personality change occurred after he was bitten by a genetically-altered spider (Kenny stepped on the spider after that). He was "proven wrong" when Kenny kicked Peter to demonstrate his reflexes, but Peter caught on and took the hit, even forcing tears. Despite that, he still believed Peter was Spider-Man and kept it to himself until their classmate Liz Allan's mutant powers manifested, at which point he let Peter know that he knew.
In Marvel Adventures Spider-Man, Emma Frost and one of her friends find out that Peter's Spider-Man due to Emma's psychic powers. Cue Peter Parker Held Hostage where she psychically manipulates a group of thugs to assault Peter's high school. She later decides not to blab once they find out that the reason Peter's Spider-Man is because of his tragic past.
In a classic Frank MillerDaredevil arc, Daily Bugle reporter Ben Urich discovered Daredevil's secret identity of Matt Murdock, and considered reporting it. He ultimately decided that New York needed Daredevil more than he needed a Pulitzer. This subplot was also featured in the movie.
Later, in Brian Michael Bendis' Pulse, Urich revealed to Peter Parker that he had deduced his secret identity of Spider-Man.
It is sometimes suggested (but never outright stated) that DC Comics' two most prominent heroes have supporting characters who know, or strongly suspect, the hero's secret identity. It's implied that they know, and that the heroes know they know, but that no good would come from any of them actually speaking about it openly:
Commissioner Gordon, a skilled veteran detective, for Batman.
At the end of Batman: No Man's Land, Bruce takes off his mask in front of Gordon to regain his trust. Gordon refuses to look at him and says "If I wanted to know, I could have discovered it ten years ago. And for all you know, I did. But that's not the point."
At the end of Batman: Year One, an (unmasked) figure who Gordon realizes is the mysterious Batman out of costume, has just saved his infant son and hands him to Gordon. Gordon makes a comment about not being able to see anything without his (at the time knocked-off) glasses. No one who can be a street cop has eyesight that bad. In this case justified because Batman is wanted by the authorities, so both of them know it's better for Gordon to have an excuse not to recognize Bruce Wayne.
Perry White, a crack investigative reporter, for Superman.
In the New 52, Two-Face reveals that he knows that Bruce Wayne is Batman, but never outed him, and has actually been convincing himself not to kill Bruce.
In Spider-Girl, one of May Parker's classmates thinks he's a secret keeper for Spider-Girl, but he picked the wrong girl!
In Birds of Prey, Barbara Gordon reveals to her father, Commissioner Gordon, that she used to be Batgirl and is now Oracle. It turned out that he had already known about the former, but not the latter.
Booster Gold's entire thing is playing up that he's a fool so that he can correct anomalies in the time stream. The fact that most people see him as an idiotic Glory Hound is what keeps him from being killed in his crib by evil time travellers. However, it is later revealed that Batman has known for quite some time that Booster is more important than he lets on, as the pictures the Joker took of Barbara Gordon in The Killing Joke show Booster trying to save Barbara Gordon. Batman doesn't tell Booster that he knows until Booster is as old as he is in the pictures. After he reveals to Booster that he knows, he offers Booster his friendship and becomes a normal Secret Keeper.
Chrom in Fire Emblem Awakening fanfic Pretender knows Robin's true origins, that he's Plegian and Validar's son, long before Robin himself finds out in the hopes that keeping him out of the loop will help him stay away from the darkness of his past.
In Gattaca, the hero Vincent Freeman steals the identity of another man in order to avoid the inevitable genetic discrimination that would bar him from his dream mission of flying to Saturn's moon, Titan. He forges urine samples, blood tests, and physical exams for years when a surprise exam reveals that the resident doctor has known he was a "borrowed ladder" all along, but he looks the other way because he himself has an "inferior," natural-born child.
In The Dark Knight Rises, GCPD Officer John Blake deduced the identity of Batman many years ago, and never let on that he knew until Commissioner Gordon was hospitalised by Bane, at which point he took it upon himself to convince Bruce Wayne to come out of retirement.
In Amen, Nazi Protagonist Kurt Gerstein and his wife might be an example of this, as they believe their maid Mrs Hinze may be Jewish, but do not relay their suspicions to the authorities or to Hinze herself.
Man of Steel seems to feature this, as Clark spends a good amount of time demonstrating his feats of strength during his youth in Smallville (at one point lifting a bus full of kids out of a lake to save some of his classmates). One could only assume that the citizens (or at the very least Pete Ross, his childhood friend) were able to connect the dots that he is, in fact, the alien that goes on to confront Zod.
In Spider-Man 2, it's implied Aunt May realized Peter was Spider-Man after he saved her from Doc Ock during their fight at the bank. She never directly confronts him about it, but some of her conversations with Peter later in the movie and in the third film hint that she knows.
The Deryni Duncan McLain continued the secret begun by his grandparents: his mother Vera was the fraternal twin sister of Alaric Morgan's mother Alyce deCorwyn. In 1121 he thinks only himself, Alaric and King Kelson know this, so he's shocked when a stranger who looks like Saint Camber greets him on the road to Coroth with the words, "Hail, Duncan of Corwyn."
Vorkosigan Saga: It is revealed in his parting words to Miles, after announcing his retirement in Brothers in Arms, that Ky Tung has figured out who Admiral Naismith really is. Bel Thorne also reveals in Mirror Dance that it's known for some time too.
In Blood's Pride, Jachid and his mother have been keeping the source of Meiran's illness secret from her, but in reality, she has known it for a long time. She understood why they didn't want to tell her, but still expected them to eventually trust her enough to do so. They didn't, and she left without ever telling them that their secrecy was both a) pointless; and b) the cause of the rift between them. Later, the tables are turned and it's Jachid being kept in the dark - he only understands why when he realises that Meiran knows about his own lack of honesty. Why should she trust him, she asks, when she waited in vain for him to trust her?
Live Action TV
In Mahou Sentai Magiranger, Yuka Yamazaki, the love interest of red ranger Kai, starts the series as his crush before getting her own crush on Magired a few episodes in. During The Movie that takes place a little more than halfway through the series, she figures out that Kai and Magired are one and the same, but never admits it to him over the course of the rest of the show. She simply makes occasional vague jokes, turns on the flirting a bit more, and quietly prays for his safety in the more dangerous battles.
Tensou Sentai Goseiger has Nozomu Amachi as the team's official Secret Keeper, with his father, Professor Amachi, seemingly oblivious to the fact that Alata and his friends are Gosei Angels. Towards the end of the series, however, when Eri must use her Magic Music to heal Nozomu's injuries, Amachi reveals that he has known for some time who the Goseigers really are.
Zyuden Sentai Kyoryuger has Yuko and Rika Fukui, sister and niece respectively of Nobuharu Udo, aka Kyoryu Blue. Rika was the first to learn of her uncle's secret identity, while Yuko was kept oblivious for a short time until a determination speech Nobuharu says as Kyoryu Blue secretly tips her off. While Rika openly accepts her uncle's role as a superhero, Yuko decides to keep the information to herself, instead insisting on calling him "That Blue Guy".
In the finale of The Secret World of Alex Mack, Alex learns that the truck driver who doused her all those years ago actually knew who she was, but never said a word.
Alex Mack: You knew, didn't you? You knew this whole time that it was me, but you didn't say anything because you knew I didn't want you to.
Dave Watt: Yeah.
Dave: You're welcome. (Alex gives Dave a hug in gratitude)
Dave is actually lying. He didn't know the whole time: there was an earlier A Day in the Limelight episode where Dave manages to figure it out but decides to keep the secret, learning by that point that Danielle and Vince considered her as evidence of their illegal activities and had no qualms about silencing her.
Dave: [watching from a distance] Don't worry, Alex. Your secret is safe with me.
In Smallville Chloe plays this for the second half of the fourth season.
Lois is one of these from the season nine finale until episode five of season 10. During a good portion of season ten (even after he finds out that she knows) there's a hilarious level of Lois trying to hide Clark's identity from characters who already know it, like Chloe and Tess. (Which becomes particularly funny in Patriot where, as below, it becomes pretty clear that the others are just screwing with her. Just look at the smirk on Tess's face when Lois covers for Clark's absence to her... his Mission Control. It is possible that either Tess didn't know that Lois was in on the joke, or she was protecting her own secret, but given that this is Tess, it's quite likely that she's just enjoying Lois's attempts.)
Lois does this earlier with when she finds out Oliver Queen is Green Arrow and tries to keep his secret...from Clark and Chloe. At some points it looks like all three are just screwing with her.
Lionel Luther was one also, having the knowledge both of Clark's abilities and his birth name due to exposure to a Kryptonian artifact. In one episode, he goes out of his way to acquire surveillance footage showing Clark using his abilities (and his watching it without a hint of surprise and with a promise to keep Clark's secret safe serves to inform the audience of his knowledge). He only becomes a standard Secret Keeper after he is trapped in an elevator with Clark's mother, and Clark is forced to rather blatantly use his abilities to save them both.
In one episode of Disney's Zorro, Diego is waylaid by a Zorro impersonator. When he defeats and unmasks the impostor, he discovers it's his father, Alejandro, who admits he's known the truth about his son's secret identity for a long time - and just stopped him from making a terrible mistake.
On Grimm, it takes about a season and a half for Nick to find out Captain Renard knows he's a Grimm.
Power Rangers Lost Galaxy: Once or twice, Commander Stanton and Terra Venture's ruling council are hinted to know who the Rangers are. At the very least, High Councilor Renier pointedly cut off any questioning of where Mike had been when he suddenly reappeared after having been gone since the second episode.
From El Goonish Shive, Nanase's mother knows quite a bit about Nanase's magical ability, but doesn't want this knowledge to become known, even going so far as to have a government agent convince Nanase to continue keeping magic a secret from her family.
Non-Supers example: Haley and Roy from The Order of the Stick have both caught on that Belkar is only faking his alignment shift away from Chaotic Evil, but have agreed not to call him out for it, preferring how he acts now.
Which becomes an inversion at times, when he really shows signs of character development, but is promtly ignored because everyone thinks he's faking.
Danny Phantom: Danny's sister Jazz found out his secret halfway into Season 1, and believed that Danny would tell her when he was ready. This led to such lines as "You go... somewhere I can't see you and get help!" Her knowledge is eventually revealed midway in the second half of Season 2, and she becomes a Sixth Ranger.
Juniper Lee's brother Dennis knows of the magical world all along. Until "Sealed With a Fist", he hadn't believed it or known about his sister's role.
In Hey Arnold!, Brainy stalks Helga whenever she goes, and thus knows all of her secrets. However, Helga doesn't seem to realize it, despite talking openly about her secret love in front of him. Nevertheless, Helga keeps punching him in the face. Running Gag much? It's been implied once or twice that he may or may not think she's actually talking about him.
Greta, Zick's mother, is this in Monster Allergy when she doesn't tell Zick that she can also see monsters until she is ready to.
In The Spectacular Spider-Man, it's become increasingly obvious over the second season that Captain George Stacy knows that Peter is Spider-Man and is covering for both identities when necessary. A borderline case as Peter has by now been given more hints than he needed to figure that out for himself, but neither of them have gone so far as to say it outright.
Actually, the boys don't even realize there's a secret that requires keeping.
In X-Men: Evolution, Amanda Sefton briefly sees Kurt with his image inducer turned off and using his teleporting powers once. This increases her interest in him and she tries to pursue him romantically. She eventually reveals (during an emergency) she knows about him, and then just becomes a regular Secret Keeper for the existence of the mutants until The Masquerade is broken.
Queen Marlena in He-Man and the Masters of the Universe (1983). Several episodes hint at her knowing Prince Adam is He-Man but she never quite comes out and says it. On at least two occasions she has deliberately put her son in a position where he can help people as He-Man.
Twist to the formula in Young Justice. Instead of a civilian keeping the superhero's secret, Artemis has her superhero teammate, Robin, keeping the fact that her immediate family is all supervillains and that she's not really related to Green Arrow secret. This does not, however, stop him from trolling her with the knowledge. Artemis is actually terrified of what everyone will think of her if her secret comes out, so its pretty cool of Robin that he's known all along but has trusted her completely from the beginning.
Red Arrow knows that she isn't who she claims to be, but has let her know this and says that though he doesn't trust her, he does trust Batman and Green Arrow (who obviously know everything, possibly so do the rest of the League) and won't tell the team.
Also Superboy to Miss Martian. He knew she was a white Martian before they even became a couple, but he decided to let her tell him when she was ready.
In Batman: The Animated Series, Barbara Gordon attempts to come out to her father as Batgirl. Before she can state it outright, he heavily implies that he already knows, is proud of her, and doesn't want to "officially" know.
In TRON: Uprising, Able (the boss at Beck's garage) seems to be awfully tolerant of Beck's frequent absences and strange explanations for those absences, as well as quick to scold Zed when he expresses frustration with "The Renegade's" antics.
In "Grounded", he finally lets Beck know he knows.
Able: What I have to say, I hoped I'd never have to say. So here goes. How did you become the Renegade?
Implied in an episode of Batman Beyond. When Terry unmasks himself to reassure a kid he's rescuing, Cobra later tracks the kid down and checks his memories for Batman's true identity. The resulting image is Batman with the head of the kid's action figure, which Terry takes to mean that the kid didn't see his face well and subconsciously replaced the image. As proof, he walks over to the kid's soccer game and mentions to Maxine that he sees the kid everyday, and he hasn't figured it out. The last shot, however, is the kid looking back and giving a knowing smile, implying that he does know but kept it secret.
It's been revealed in the comic adaptation that Dana Tan knew about Terry being Batman before he revealed it.
And Word of God indicated that Bruce knew for a long time that Terry is his genetic son long before Terry figured it out for himself.
Star Wars: The Clone Wars subverts this: Anakin's super-powers are public knowledge, but he has a Secret Relationship with Padmé. The Season 5 finale implied that his former Padawan, Ahsoka has figured it out, but kept quiet, revealing it to Anakin only when she departed from the Order. Word of God confirmed that she knows about them, but didn't specify how much.