SecretSecretKeeper / Video Games

Avencast: Rise of the Mage has Gorlin, who knows the backstories of the player, the Arch-Enemy, the Big Bad, and all the conflicts between. He sees no reason to divulge anything until the absolute last minute.
Batman: Arkham Knight:
- Late into the game, the titular Arkham Knight reveals that he knows Batman's identity as Bruce Wayne and kept that fact to himself until he believed he finally had Batman cornered (including mentioning that he didn't tell Scarecrow). It's because he's a former Robin, none other than Jason Todd.
- As Batman and Gordon are on their way to confront Scarecrow, Gordon references taking Bruce's statement after his parents' murder and outright calls Batman "Bruce". It's left ambiguous if he's known Batman's identity for some time or if he put two and two together after Jason called Batman by name.
Batman: The Telltale Series: John Doe is revealed to have known that Bruce Wayne was Batman for some time. Initially, he wasn't completely sure, he just heavily suspected, but when the Bat Signal appeared in the sky while they were at a restaurant and Bruce almost immediately made an excuse to leave, he was sure.
Dustborn:
- Pax is keeping her pregnancy secret from the rest of the crew. In Issue 7, she fears she may have harmed her baby while testing out a new Vocal, only for Noam to step in and reassure her that her baby is fine. It turns out Noam figured this out sometime after Issue 4, but didn't tell Pax.
- Girl is the third party member to realize Pax is pregnant, as shown when she holds her ear to Pax's belly while the latter is asleep. However, she never discusses this with Pax due to being mute.
I Was a Teenage Exocolonist: Getting close to Cal triggers a Secret Pet Plot in which the pet is eventually discovered by the colony's autorities thanks to Gigantic Adults, Tiny Babies applying to its species. During the discovery scene, Flulu, who is both the protagonist's strict mother and Cal's boss, turns out to have known of the pet all along and tolerated it for the time it proved to not be dangerous.
Archmagus Rubus, in Queen at Arms, figures out early in their acquaintance that Marcus is female. However, he only tells her he's known all along if his romance path is pursued; otherwise, he doesn't mention having made the discovery.
Near the end of Octodad: Dadliest Catch, it's revealed that Stacy has always been aware that her father is really an octopus masquerading as a human. Played with in that Stacy didn't even know this was a secret; she just never mentioned it because it was so blatantly obvious that this was the case that she assumed Everybody Knew Already.
There's a journal entry in Red Dead Redemption 2 in which Arthur says he knows fellow gang member Bill is living with some sort of secret about himself. He doesn't know what exactly the secret is but he respects Bill's privacy and doesn't believe it's his place to prod. The game itself heavily implies said secret is that he's gay but there are other people in the gang who have their suspicions as well.
In Super Mario Sunshine, Bowser tricked his son into believing that Princess Peach was his mom so that he'll help kidnap her. In the ending, Bowser Jr. reveals that he knew all along that Peach wasn't his mom, but that the adventure was so much fun that he'll continue scheming with his father to defeat Mario regardless.
If you choose to play as a girl/other in South Park: The Fractured but Whole, Wendy reveals to your character that she knew the entire time during South Park: The Stick of Truth, but kept quiet about it because she believed you wanted to be mysterious, and wanted to respect that.
Spider-Man (Insomniac):
- Spider-Man (PS4):
  - In the final boss battle, Doc Ock addresses Spider-Man as "Parker", revealing that he'd either slowly figured out, or always known, that Peter is Spider-Man and not just his gadget guy. Peter is absolutely furious when he realizes the implications that Octavius had done all his evil deeds knowing full well his lab assistant is Spider-Man, and his hopes of getting through to his former mentor are shattered.
  - Aunt May reveals at the very end that she's known Peter was Spider-Man for quite some time by telling him "I want to see my nephew". Unlike the comics she isn't in denial about it and is proud of Peter helping people, and kept it a secret so he wouldn't worry about it (which makes many earlier scenes in the game much more heartwarming). It's a cold comfort for Peter however, as she's on her deathbed.
  - In the "Hidden Backpack" side quest, Peter finds the backpack holding Matt Murdock's business card, who gave it to Spider-Man one day in case he ever needed a lawyer. Peter is perplexed at how a blind guy knew who he was.
- Marvel's Spider-Man 2: In The Stinger, Doc Ock isn't willing to tell Norman Osborn who either of the Spider-Men are.
Star Wars: Knights of the Old Republic: After The Reveal that the Player Character has been a brainwashed Darth Revan all along, most of your crew takes the news pretty hard — except for Jolee Bindo (if he has already been recruited). When confronted, Jolee admits to having immediately recognized your face when you first met him on Kashyyyk (he has, after all, met you before during the Mandalorian Wars) but decided that keeping his mouth shut was the least harmful thing to do at that point.
Sticky Business: In Book of Shadows, Francine's friend group is strongly convinced that her best friend Hilda's a witch, but Francine's afraid to ask for her help out of fear that Hilda might think she'd be exploiting her magic and that their friendship is transactional. After seeing Hilda magically repair Francine's artwork without any prompting, Francine asks you to keep it a secret between them.

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