Elias is still there when Jon comes back from having a cigarette at the end of season 2. Elias then takes Jon captive. He uses the fact the police think Jon murdered Leitner and are tracking him down as well as recordings of Tim and others talking angrily about him and Jon's own paranoia to make him believe staying with Elias is his best option. Stockholm syndrome and grooming Jon to be his perfect Archive (and wife?)