Not all minions are evil. Some simply don't know better, either due to stupidity or just naïveté.
- In Neon Genesis Evangelion, the entire staff of NERV, a Mildly Military multibillion international governmental organization, are, unwittingly, the minions of a Mad Scientist who plans The End of the World as We Know It once they're done preventing others from doing it.
- In Slayers: The Motion Picture, Naga momentarily ends up on the wrong side; unaware she's working for bandits until Lina spells it out for her. Though Lina's hardly got room to talk.
- In Street Fighter II V, Cammy is sent to assassinate Chun-Li's father. However, she's not doing it out of malice. She is informed by Shadowloo agents that her target is actually a high-ranking criminal that needs to be dealt with.
- Kyoko from Black Cat. She's a ditz that doesn't even know what the Apostle of The Stars (the organization that plans to take over the world, by the way) is. Nevertheless, she still follows them. She pulls a HeelFace Turn after falling for Train.
- Yui from Fushigi Yuugi counts as this with her being deceived by Nakago into thinking Miaka is the evil one.
- Rosario Vampire: Brightest Darkness:
- After his initial escape from his master, Dark was recruited by Kiria into Fairy Tale, who claimed he could be a hero to the world by joining them, quickly becoming their top agent. However, Dark was completely unaware of Fairy Tale's true motives until he discovered they planned to destroy Yokai Academy for teaching human/monster coexistence; outraged at being used, Dark erased all data related to Yokai Academy from Fairy Tale's computers and destroyed the base he was stationed at before taking his leave.
- Similarly, Akua and Kahlua only worked for Fairy Tale because they genuinely believed that the extent of Kiria's plan for the Chrono Displacement spell would simply be to use Tsukune's ghoul, infected with Blackheart, to rewrite the Battle of Kahdaln in favor of the monsters, which would give their father a leading place in the new world rather than being confined to The Masquerade. By the end of Act III, they have to be specifically told that Kiria's plan wasn't just to do that, but also to wipe out Issa Shuzen himself by infecting his daughters with Blackheart and sending them back to destroy his empire from within, as well as to wipe out the other Dark Lords and anyone else who could oppose him, thus rewriting history entirely in Kiria's own image. Upon learning this, Akua and Kahlua are horrified and spend the entirety of Act IV trying to atone. Gin even lampshades this trope, telling Akua and Kahlua point-blank that they were "too stupid to realize they were being used."
- In Street Fighter, Zangief doesn't become aware that Bison is evil, until Dee Jay tells him; which prompts Zangief to ask why Dee Jay was working for him, since he knew.
- Every human law enforcement officer in The Matrix is this, uncomfortably overlapping with What Measure Is a Mook?.
- Becomes a Conversed Trope in Clerks, where the characters have a spirited debate about whether the contractors building the Death Star were Ignorant Minions whom the Rebel Alliance murders or knowing parts of the villainous Empire.
- Alias: Most of the people working for SD-6 don't know it's a terrorist organization, they think they're working for the CIA.
- In Battlestar Galactica, Boomer didn't consciously know she was a Cylon at first, and was a sleeper agent within the fleet (who was triggered to do a couple acts of sabotage by Cavil using a sort of hypnotic suggestion involving a carved trinket, then "re-sleepered", as revealed in the movie The Plan). After she was fully conscious of what she was, she ended up in a HeelFace Revolving Door throughout the show, as her human experiences and Cylon nature conflicted.
- In the B movie and Mystery Science Theater 3000 episode I Accuse My Parents, young Jimmy starts working for local gangster Charlie Blake without realizing Charlie is a gangster. He thinks he's just delivering legitimate messages and packages. Considering the fact that Charlie looks, talks and acts like a gangster, this plot point is not too believable.
- For much of the fourth season of Babylon 5, Garibaldi, having gone through a More than Mind Control experience, is unaware that he is essentially working for Bester, in an operation to infiltrate tycoon William Edgars' organization which is developing a biological weapon against telepaths. When he finds out in a Just Between You and Me speech by Bester, there's a Big "NO!", and from there he works for the day he can get revenge on him for using him, probably especially because it caused him to betray a good friend along the way.
- Mr Endawi of EarthForce intelligence comes aboard B5 to ask questions about the siteing of a shadow vessel unaware that EarthGov has been suborned and that he is being used indirectly by the shadows to find out what their enemies know. None of the actions he takes or the questions he asks are unreasonable and he would have no possibility of knowing what he is being used for.
- An episode of That Mitchell and Webb Look parodies this trope with two SS officers. One asks the other if they're the bad guys, and points out that their uniforms have skulls on them.
- Bobo and Uncle Deadly in The Muppets (2011), at least initially, as indicated by the page quote.
- StarCraft II: Nova's campaign has her carry out a few missions for the Defenders of Man, unaware they're actually using her for False Flag Operations that will kick Arcturus' son Valerian from power, seeing him as an usurper. Fortunately she manages to find out the truth rather fast and overturn them.
- The Freelancers in Red vs. Blue think for the longest time that they're fighting the good fight, their boss the Director is a good guy, and the Insurrection are the bad guys. Not quite. Some of the Freelancers do eventually experience a Conspiracy Redemption.
York: I felt it since Texas showed up. And when cops and military started shooting at us, yeah, I find I just keep coming back to the same question in my head over and over again.
North: And what question is that?
York: We're the good guys... right?
North: Yeah, of course we are.
York: You don't sound so sure of yourself.
North: No. No, I suppose I don't.
- Clippy from Freefall sincerely believes he's acting in humanity's best interests. Unfortunately, Mr. Kornada has manipulated him to believe that his best interests are the same as humanity's.
- The Monster in the Dark in The Order of the Stick talks like a naive child who has no idea what Xykon and Redcloak are up to.
- Penny from The Mighty B!, whenever she's hanging out with Portia and Gwen instead of Bessie.
- Da Bears from Adventures of Sonic the Hedgehog were this in their first appearance when Scratch and Grounder tricked them into thinking that they were Sonic and Tails and that Sonic and Tails were Scratch and Grounder.
- Stegmutt from Darkwing Duck was this to Dr. Fossil at first. He had no idea about his master's true intentions, until near the end of the episode.
- Valerie from Danny Phantom, who doesn't realise Vlad is a villain until season 3.
- In The Simpsons episode "You Only Move Twice", Homer takes a job with an affable new boss, completely unaware that he's a Bondian supervillain trying to Take Over the World (and partly succeeds), not even noticing when he quits in the middle of a firefight. The real clincher is arguably that Homer helps recapture a James Bond expy, is within earshot of him being killed by automatic gunfire, and he still doesn't realize what his boss is up to—Homer though that was just another employee getting chewed out for being lazy. He is even in the room when said boss was giving his evil speech, but is occupied with the candy machine.
Homer: Say, what's going on?
Hank: I'm having a little trouble with the government.
Homer: Oh, those jerks always walking over the small businessman.
- In Teenage Mutant Ninja Turtles (2003), Hun had no idea until "Exodus: Part 1" that the Shredder was an Utrom. In fact, the only Foot member who knew this was Karai.
- Teenage Mutant Ninja Turtles (2012): It's eventually revealed that both Dogpound and Karai have been tricked by the Shredder. They were led to believe that Splinter was the one who betrayed Shredder, rather than the opposite.
- Avatar: The Last Airbender: A lot of the Fire Nation people are arguably like this, as Fire Lord Ozai has a personality cult around him, apparently.
- TRON: Uprising: Paige is Tesler's loyal Dragon because she was tricked into believing the Isos slaughtered all her friends and patients at the medical center where she worked, blaming herself for the deaths because she treated their injuries instead of turning them in. The reality is that Quorra knocked Paige out when the Occupation troops arrived so she would be spared while Tesler's troops were the ones who marched through and killed everyone.