I read this a long time ago, so I can't remember much.... The main character was originally part of a resistance movement or something from the slums, and they are trying to take over a government facility for some reason. Somewhere along the way, main characters gets his ass kicked by this girl (whom he later befriends) and loses consciousness. He wakes up, and he's completely changed, head to toe because a government scientist turned him into a humanoid cyborg in order to save his life and make use of him. And it turned out quite a long time passed before he woke up because his little sister who got left behind has already grown up and joined the resistance group. He has to fight her when the group infiltrates the faculty again. Or something like that. That's about all the useful stuff I can remember, though it may not be entirely accurate. Please help if you can? Oh, and this is probably one of those action-type shoujo manga because I remember the drawings were pretty geared towards girls.

Possibly Mother Keeper

Oh yea, that's it! Thanks~ :]