After that infamous lacrosse game in season two, Gerard kidnapped Stiles. Instead of letting him go, he faked Stiles' death. He then handed Stiles over to another group of hunters who then worked and worked to wipe his brain and make him the perfect weapon to eliminate threats. Everyone thinks he died until he's assigned to Beacon Hills.
I do not own teen wolf. And I got the plot idea from a youtuber- XSilentHarmony.