 At the end of the episode, it is shown that the entire thing was in fact a dream about an alternate time line that Booth had while unconscious and part of a new book Brennan was writing.Zack also returned in the 100th episode as a flashback to Booth and Brennan's first case together.Later on, Hodgins says that Zack will be in the asylum "forever", hinting that Zack would be in the asylum on a permanent basis and would never be released into the general public.