Warning: Spoilers for Terminator Genisys are in play below. If you have not seen the film yet, please bookmark this page and come back after you've seen the film.
For the entire run of the Terminator franchise, the bedrock of the story has always been the fact that one day, John Connor would rise to rule humanity's resistance against Skynet. He was the ultimate victor in the war against the machines, and the one target Skynet kept sending agents back in time to destroy. Of course, that's all changed now thanks to the new version of Skynet we see in Terminator: Genisys. Thanks to the alternate universe Skynet, colloquially known as "Alex" if you go by the entry on IMDB, John Connor is now the bane to humanity's existence, as he is now partnered with/controlled by Skynet itself. Which raises the ultimate question in the new Terminator franchise: what is John Connor's future in the series?
I was able to speak to Jason Clarke himself last weekend, and even he's not sure how exactly John's story will change from this point. However, Clarke did confirm that he is indeed on contract for the next two Terminator films, so the question of if John Connor is coming back isn't an issue. But even he is in the dark as to how John will feature into the future of Sarah and Kyle's journey in the next two Terminator films (should they come to pass). All we really have to go on is what Clarke said about the future of the character, which includes the following statement:
I think he’s still a fascinating character to explore. [... And] I know they’re up to something.
With the certainty that John will return, and the uncertainty of how he will return, we can at the very least speculate what the future of the new John Connor / T-3000 will lead to. And to be able to do that, we need to focus on the curveballs that Terminator: Genisys throws in the way of the original timeline, most importantly the fact that Sarah Connor is now the implied "savior of humanity." Since the T-1000 and Pops entered the equation in 1973, Sarah has basically fulfilled the role of training to become humanity's protector on this alternate timeline. This basically renders John obsolete, and jeopardizes the actual John's future. Because Sarah and Kyle never "mate," John actually HAS no future.
The "new and improved" John, however, can still exist.
The John Connor we know from the previous Terminator series is dead... at least, for the time being. Without Sarah and Kyle "mating" back in 1984, John now only exists as the robotic killing machine that Skynet created out of him in 2029. What's more, since Skynet survived the attack on San Francisco campus it was born on, it can always rebuild John from scratch and use him for its nefarious purposes. Much like Sarah has become the new savior, John has become the new harbinger of humanity's end on this recalibrated timeline, and through the next two films we'll probably see him act as a nemesis to Sarah. No matter how hardened they become, there's always going to be part of Sarah and Kyle that wishes John never turned out the way he did. That weakness will always be at the heart of Skynet's attempts at world domination, and will exploit for as long as it takes.
Of course, there's always the possibility that, like in the previous Terminator timeline, John Connor may have left behind an arm for the Dysons to revamp their robotics program with. After all, he was reaching out of the time displacement machine as he was being obliterated. Even worse is the fact that when he had his mother captive, John dug into Sarah's skin with his finger. There's a very good chance he left a little something behind that would either convert Sarah into a T-3000 unit, or might allow her to give birth to him once more – whether she wants to or not.
There is no shortage of ways that the Terminator franchise could bring John Connor back from the dead. They've done stranger things before, and continue to do even stranger things today. So don't be surprised if the next couple Terminator films feature a familiar face, because even Jason Clarke knows that there's still material to be mined in the battle between man and machine.
Terminator Genisys is in theaters now.