Basically the question, “Will You Join Us?” is the key. Future John reached out to the Liquid Metal species and they rejected him. Gaining or losing their loyalty was a key turning point in the war.
At some point T1000 Weaver realized that rejecting Connor’s offer was a mistake. She goes back in time to create a counter Skynet AI, which ends up being John Henry. She believes this will help John win the war, or at least turn the tide. At first I thought John Henry existed in the future, but there was a lot about him that Weaver didn’t know. As time went on, it became clear that she was constructing John Henry on the spot. So this was John Henry’s first appearance in the timeline. Weaver wanted peace between Humans and Metal…maybe she came from far enough in the future to see both species destroy each other and most of the planet as well.
Cameron clearly knew the significance of the phrase, “Will You Join Us?” Cameron also knew that John Henry needed to get to the future, mobile, in order to help John win the war. That’s one reason why she was in the present and thus gave him her chip. If she got sent back by Future John, he knew all of that. He sent her back both to ensure his own safety, and ultimately to be sure that John Henry made it to the future.
If Cameron sent herself back, it’s entirely possible that she either killed John and was trying to fix it, or John got killed as a result of their unorthodox relationship. The theory that I like the best is that other resistance leaders that thought like Jesse eventually mutinied against Connor. One way or the other he ended up being killed, and it was all because of Cameron. She realized then that her presence would lead to John’s death one way or the other, and sent herself back.
So: John Henry and his mother, WeaverBot, arrive in the future. They’ve got the idea of creating a peaceful coexistence between humans and metal. Cameron’s dechipped body is in the past, thus getting her out of the picture, and allowing John a future without her.
The only wrinkle in that scenario is the fact that teenage John came with Weaver in the time bubble, which effectively changed everything, so I don’t know how that would’ve played out…I know that Thomas Dekker has said that John would’ve come back to the present about midway through Season Three.
Really would’ve been great to see that storyline get its proper conclusion.
HINT: DO A MOVIE LIKE THEY DID WITH FIREFLY/SERENITY!!!