Does it count as spoilers if its in the damn trailer?
Ok so John is shot! Oh no! Oh wait he is some kind of nanomachine construct so he is fine.
John says he is neither man nor machine, so I’m guessing Skynet just got sick of all this temporal nonsense and fate and yadda yadda, decided to not kill John but help him instead and have created this man/nanomachine hybrid.
Then John goes back in time to spread this organic/machine goodness to all humanity whether they want it or not. Basically John is the villain.
They played with this concept in TSCC.