We find out early on that the original John Connor was never the son of Sarah Connor, but just some random guy who rose to the challenge and became the leader of the human resistance. Knowing that the machines had developed time travel, he adopted the name and history of some random dead guy and leaked this to the machines, knowing they would go back and try to kill them. He sent Kyle back to protect them, with the plan of conceiving John Connor and raising him up as an even better leader.

Cut back to the future war, and now there are two John Connors.