Cartesian Karma

So your characters were previously brainwashed, betrayed the heroes, went on their own sort of rampage and needed saving to return to their ideals. Luckily, the good guys manage to accomplish this through laborious amounts of screaming, fighting them, and friendship power. And now that character is back to normal, yay! Everything should be all strawberries and hotcakes, right? I mean, they've clearly come to their senses and are back on the right of things.

Well unfortunately not always. There are always some possible problems with characters regaining their focus that have to be faced.

Simple problems might be that relationships are strained, as other people might not be quite so eager to forget the character's actions off the bat. A character who has crossed the moral horizon line obviously won't as be easily redeemed, even with the all-forgiving power of friendship.

More problematic is that the characters aren't completely back to normal, and traits from their former self may still linger on even after they've overcome their vices. Can this get any worse? It can.

The most problematic issue becomes when a character essentially has to live up to their actions and face the music, thus being dealt Cartesian Karma. After all, sure it's great that they're not trying to eat your soul, kick puppies, or burn down that orphanage any more, so what's the deal?

Unfortunately in failing that, they still managed to kick a few kittens, and rob the local grocery market. And law enforcement isn't exactly ready to take 'I was brainwashed by a Super-villain/mind-virus' as a valid legal alibi. Also anybody 'normal' seeing you in your altered state might be equally hard to work out, especially if it's not something you could explain without telling too much. The consequences of one's actions simply don't vanish when the mentality causing them does, so even mind-controlled character's have to face some sort of retribution, like it or not. Except whenthey don't.

What's more, who's to say you were just eating children and playing hopscotch during your brainwashed-existence, and not having to face any serious danger or genetic experiments? Any damage sustained, bodily changes or physical alterations aren't going to go away just because you've come to your senses. Those are going to have to be faced as well. If brain-washed you had eaten a few to many donuts in the baddies' hideout, you're simply going to have to live with his/her sustained diabetes.

In cases where the dealt karma is so major the character can't persist, it often leads to death, heroically or tragically.

Can lead to My God, What Have I Done? moments, even Out, Damned Spot! if the character feels perpetually guilty by their previous actions upon being dealt Karma. A heroic or moral enough character, if determined and truly guilty, will probably try to reconcile with their past actions in order to fix their record and deal with the situation.

Anime & Manga

 * In Naruto, Sasuke's fall and betrayal of konoha has continually been a plot point, with the eponymous character constantly hoping for his return. Obstructing this is not only the fact that he's now an internationally wanted criminal, but also had a central antagonist absorbed into his body at one point, and he had gone nearly blind.
 * Yomi goes through this in Ga-Rei Zero, with her going beserk and only having Kagura to stop her. In the anime it ends tragically.
 * The entire concept of Shissouseiki victims often plays into this.
 * In the Chrono Crusade anime, Joshua after having Chrono's stolen horns removed is able to revert back to his old childish self. The problem is, he becomes essentially 'locked' in that state, perpetually having the mind of his 12 year old pre-horn self. He fairs much better in the manga though.
 * Tacitly averted in Zatch Bell with Koko who was sadistically brainwashed, but is later rescued by Sherry and restored back to her original, kind innocent state. It's a good thing she's not a wanted criminal now or anything and can happily go to college too, especially after (publicly) razing most of her town and kidnapping dozens of people. It would have to be inferred that her savior Sherry has some pretty good connections.
 * In Pysren, Tatsuo refuses to return to the past even after being freed from the mind-control induced on him. It's probably a factor that the artifact that was controlling him is still embedded into his body, and he'll die if it runs out of energy.
 * Possibly subverted in Hunter X Hunter when one of the side characters gets kidnapped by the ants, brainwashed and altered to be one of them. She's eventually comes to her senses, and as Killua points out, her entrusted one Gon is not one to judge, and it helps the Hunter organization itself isn't one to persecute her just because she's now a chimera ant.
 * Also it's a pivotal point played straight with Gon. Blinded by his rage he, activates a technique that allows him to rapidly age/grow and defeat an enemy vastly superior to himself. Unfortunately after calming down, he's stil mutated and puts himself on the brink of death.
 * Also his teacher and role-model Kaito, who is made into a living rag doll for the ants to manipulate that Gon desperately wishes to bring back. The realization that

Film

 * The realization of this was the most likely factor in Darth Vader's acceptance of his death at the end of the trilogy. He had already had the majority of his body burned off and was basically encased in an armor that well being his life support, was also a symbol for tyranny and fear for people everywhere. It's also hard to imagine the rebels or improvised government not trying or condemning him after.
 * In the end of the The Dark Knight, this is played intentionally by the Joker in order to manipulate Dent and get him to commit enough crimes that he 'falls', and has all the blame shifted towards him, thus destroying the cities hope in their law enforcement. The bat is able to avert this only by taking on the blame himself for 2 Face's murders.

Webcomics

 * Done so in Homestuck, to a more general sense. Vriska is controlled essentially by her civilization's violent culture and expectations, her own insecurities/ego, self-destructive actions, and the rules of paradox space itself. She 'over-comes' it eventually, but by then it's rather to late for her to change. She even acknowledges she can't change what she's done by any means, but accepts it and any karma facing her because she believes she needs to do the right thing.

Western Animation

 * Although the top quote is more just a product of Peter's usual shenanigans in Family Guy than direct mind control, he has been "changed" temporarily an untold amount of times for the period of single episodes. Despite this, it's subverted as the rest of the cast usually don't see anything periodic about it and never reprimand him beyond the individual change. To date, he has been "brainwashed" into becoming feminine, "rich", Jewish, a bully, Mexican, African American, a redneck, and a homosexual, all of which are forgotten about by the next episode.
 * Also the fact that both Mayor Adam West and Meg are apparently unwilling sleeper-agent Russian spies, the former of which has been outed. No consequences of this have come up so far, but it's hard to question it when one ponders how someone as suspicious and incompetent as Mayor Adam could have become Mayor in the first place.