They woke up after blacking out again from Jake being in control. B/C Khonshu "freed" them, but he still is using Jake, as he has all along.but what about at the very end, when Marc/Steven wakes back up in his apartment?
The real trippy part is when you go back & realize how many of those blackouts waking up in the aftermath of violence was actually when Jake was in control from the beginning, including the killing of Layla's father.
