After the Ghost Riders attack, Stiles was still missing. Everyone, after remembering him, searched for him for a good time, not knowing that he was kidnapped by WCKD and that the facility wiped his memories and sent him to the Maze with the Gladers. The Gladers managed to escape from WCKD. After a month of the Gladers's escape and settling down at the Safe Haven, the FBI, including Agent McCall, found the boys and . . .
Read to find more about what happened to Thomas/Stiles. Oh! Btw, Newt is still alive (Tommy saved him) and he's dating Thomas. And s6b of TW never happened.