I am just wondering if there exist a story like this.

The protagonist is with the enemy but then switch side to the good guys or where the protagonist have some sort of connection to the enemy for example Code Geass where the protagonist family is the enemy.

(sry for bad english)

Pls no Yuri, Yaoi or Hentai.

Blue Exorcist - Our protagonist is the literal spawn of Satan
Noragami - One of the main villains so far is the protagonist's father and the switch happened before the beginning of the story
Deadman Wonderland - Not saying much because spoilers
Hoshi no Samidare - While not being with the main villain, the protagonist follows someone with villainous ambtitions, and then gradually change
Pandora Hearts - Spoilerific

My current top 3:
Fullmetal Alchemist
Pandora Hearts
3-gatsu no Lion