I'm halfway through season 3 and I pretty much get (or at least I think I do) the whole ALIE/City of Light situation/storyline, however I keep wondering how Jaha was able to see her when they first met? As far as I remember he didn't ingest a chip/City of Light key like the others do before they are able to see ALIE.
Rewatching now, she probably got the info from the missile Jaha came down on. Presumably there was Arc info stored in some code contained in the missile ALIE was Abe to access. Just a guess though, I’m here for the sane reasons as everyone else