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Feels like My God, What Have I Done? or something similar, like Unwitting Pawn. In the sense of "I thought I was doing [what I like], but wait, my actions have only been enabling [what I think is heinous] all along."
I say Unwitting Pawn because it seems likely there's some propaganda involved, that the relatively normal, patriotic person is sold on one version of the idea, but they're enabling the worse version that's not in the propaganda.
Edited by KDYes, but that's for Alice, what's the trope for Bob being such a walking argument for his side being wrong that Alice has a Face–Heel Turn?
Like, if Bob is The Corrupter, Alice eventually falls to his methods and worldview, here Bob eventually causes Alice to defect from his worldview.
For instance, Alice is part of an invading army and fully believes in its cause (revenge, preventing the spread of communism/terrorism, bringing advancement to primitives, etc.). Then she's repeatedly exposed to Bob doing things like capturing civilians to sell them to Human Traffickers (at least, the ones he doesn't keep as sex slaves), looting corpses then selling the corpses to pet food companies, mentioning that they need to finally find a solution to the vermin they're fighting, attacking with chemical weapons marked "Zyklon B" he inherited from his great-grandfather Heinrich (the one who emigrated to South America in the 40s), etc. Bob never being punished (or even being rewarded) for his Complete Monster behavior by higher-ups is what makes Alice finally realize her side is in the wrong and she deserts/defects.
Edited by Chabal2Alice's departure would be Resign in Protest and afterward she would be a Defector from Decadence, but I can't find a trope for being the guy Alice resigns in protest of.
Edited by dalek955

Alice is part of an evil organization, but believes it's doing the right thing (Well-Intentioned Extremist, The Fundamentalist, My Country, Right or Wrong, etc.). Bob is part of the same organization, but is so Card Carrying Evil / Obviously Evil / Stupid Evil / Underling with an F in PR / generally a Straw Man about his immorality that he's more a plot device to force Alice into a Heel Realization and Heel–Face Turn once she stops deluding herself that Bob and the organization's goals and methods are different.
Not Even Evil Has Standards where Alice is fully aware that she's evil from the start, or Your Approval Fills Me with Shame since Alice and Bob are already at odds with each other over Bob's methods.
- In Le Silence De La Mer, a Nazi stationed in occupied France keeps trying to convince people of the righteousness of his cause and how a better, stronger world will result once the parasites are removed. Then he meets his brother who's now more of the Rape, Pillage, and Burn mindset, and realizes that the brother is the one better aligned with the regime's goals. He asks for a transfer to the Eastern Front to get himself killed.
- In Fury My War Gone By, Hatherly resigns from the whole "preserve American interests by starting revolutions" thing when he sees that it leads to people like the gleefully evil Barracuda who openly commits war crimes, rapes and murders civilians, and sends drugs to the US all while wearing a US uniform, and even spares Hatherly and Fury since he knows they can't touch him.
Edited by Chabal2