You know, BAG's mentioning the possibility that John sent Weaver back was the final puzzle piece that I needed to connect the dots (so to speak) for this season.
I'm not 100% certain that Weaver is working FOR John, but I now think that they came up w/ this whole plan together and this also means that Josh and co's rabbit hole has hooked a sharp right and is blasting off into right field.
If John sent Weaver back in time to get her hands on The Turk, that meant that all of this had happened before...to a degree. It's possible that originally Weaver sent Cameron back just to influence John as the master plan to stop judgment day, but things still went wrong - Skynet still blew up the world.
Original timeline - Derek squealed in the basement about John Connor's location and *POOF* he was sent back to the past top get him away from the enemy. Derek's former orphaned self was left in the past while the rest of time's events shifted. In that timeline Cameron was gathering intel for the resistance and getting close to John - she went along w/ John's plans because that was her purpose as an infiltrator. The "Join us" line was probably always some sort of an "abort mission" trigger in Cameron's programming.
Derek's return fractured the current timeline and an alternate timeline was created where he was abducted and tortured in the future this most likely was payback for his torturing the guy in COMPLICATIONS. In THAT timeline Cameron and Weaver were now fully in leagues together. Jesse and her crew royally screwed up the plans of the resistance and Weaver said "Nope, sorry I'm not joining you and your disorganized band of rebels - we're going to do things differently." *Poof* A different Cameron was sent back in time at the same time that we met her - this one now has all of the knowledge of what happened the first go around and has been implanted w/ new orders.
*Poof* The big boss has to get involved. Weaver went back in time to try to stop Skynet with intel that John provided her of the leads that his family was tracking back in 2007 - that everything depended on The Turk.
She got her hands on The Turk and probably from John's intel sought out and hired Ellison. Together John and Weaver concocted that Weaver should work on creating their own Skynet that could better fight the beast that blows up the world. The intent was to create one that values human life and fight against Skynet FOR humanity. When John Henry learned about the Coltan plant, Weaver went in and took out a key stronghold of Skynet in THE GOOD WOUND.
Our current John of course was to be left in the dark to all of this, probably because John insisted that humans should be given the choice of free will to make their own decisions. It's why Cameron was always sketchy about revealing too much about the future beyond generalizatons to John.
The message sent by Ellison from Weaver to Cameron at the end sealed the fact that she was Weaver's creation/tool. The "Join us" was the trigger that told her to return to Weaver that the plan had failed and that it was time to start over again. Cameron knew that John couldn't survive in the past w/o his mother so she went on a near suicide mission to spring her out of prison. Then her programming over-wrote Sarah's orders and she gave her chip - the one chip that wouldn't self destruct and gave it to John Henry because he was more valuable to the mission than she was.
John was a moron to go chasing after her chip in the future since John Henry had downloaded Cameron's consciousness into the Turk before jumping into the future. When John jumped w/ Weaver he fractured reality again and now he's in a future where no one knows him because he didn't exist for many years. Obviously Skynet still won, leaving Sarah on her own to fight Skynet failed and Judgment day still happened.
So there's a whole world of possibilities for where they can take things for season 3.
John is now forced to become the legend. It's about time that he and Kyle get scooped up together and taken off to a Skynet prison and for his legendary status to be born with their escape.
We saw in THE GOOD WOUND that Kyle showed Sarah where she must put her photo for it to survive judgment day. Eventually John will need to get back to his own timeline because the truth is if Sarah wasn't able to stop Judgment Day then he's needed there more than he is in the future. Kyle needs to fall in love w/ Sarah though before he can leave, else he'll never survive.
Sarah and Ellison will have to work together to protect the children who were left behind. There was a reason that the Weavers were selected for this mission and Savannah seems to be the key. We have yet to learn her importance. They have to go find and save Danny Dyson as well.
In this go around either Allison will go with him back in time or Weaver will build a new Cameron for him. Derek will mostly be sent back as well because with things always looping, Derek is weak under torture - it's better for him to be in the past than in the future where he could end up compromising the complete and final survival of mankind. John Henry is the key to it all because he's going to be the one to figure out how to reprogram the Terminators for John and the resistance so that John can keep fighting and stay alive.