And why did I not think of this before?!
Cameron's chip! That's what the AI was after in To the Lighthouse! Duh. It's so clear to me now. The goons obviously knew Cameron was a machine, which is why they nabbed Derek and only fired some shots at her as they took off. Derek was the bait to lure Cameron into a trap (the water at the warehouse). No revelations there, but I always thought the AI (on the phone) was instructing the goon on how to pull her chip so they could disable her. It never occurred to me that the AI needed a chip FOR ITSELF. And not just any old chip. Cameron is "special". She has the most powerful neural net processor in the world — able to infiltrate entire traffic systems in a single bound! (Also it doesn't self-destruct when you pull it out).
Kaliba has coltan and the AI got endo schematics from John Henry when it hacked him with the worm. It had what it needed to build itself a body, but without a chip, a body would do it no good. Of course, it could've just used Cameron's body too, but y'know, John Henry said it was his "brother" so maybe advanced AIs have gender identity ;) Or maybe it actually needs to look like someone specific that's male.
So why did the AI need to be mobile? Who the fuck knows. It had the worm that could give it control of other computer systems and it had the backdoor access to military systems thanks to Fisher's handiwork. Why it would need to be a walking "human" to initiate judgement day, I haven't a clue. Seems to me everything was in place. Obviously not, though, or it would've already done it. So there's clearly more to be accomplished before the apocalypse can commence.
Onto John Henry...
He had the damaged chip from the Kaliba water cooler terminator that Weaver wanted him to try to gleen info from. I have no doubt that he succeeded in doing so and now has info about Kaliba. Perhaps he knows their targets (Savannah, himself and the whole damn human race!). Perhaps he knows their plans (apocalypse!). And perhaps he knows the current whereabouts of Kaliba (and the AI).
When Cameron enters the room, he shares this information. "My brother wanted your chip so he could [insert Kaliba master plan here]. I can stop him, but I'm tethered to this pretty box with the retconned 3 lights."
"That really is a pretty box." Cameron says. "You can put me in there and take my chip. Maybe Sarah will like me better if I have 3 dots anyway. I should probably leave John a note, though."
And this, my friends, makes my
wacky theory of old work: Neither Cameron nor John Henry are in the future. They're both still in 2009. But the writers would probably do a little better with the dialog ;)