So it’s pretty obvious that Halo 6 will build up to a major, and possibly final confrontation between John and Cortana. The question is: what will happen?
As I see it, both of them still have strong feelings for eachother (what exactly those feelings are is up for debate). Case in point: all of Halo 5 was John and Cortana trying to save eachother and contain eachother because of their disagreement. John wanted to get to her and talk sense to her, perhaps go as far as pulling her out of the Domain against her will. Meanwhile, Cortana tried to convince him SHE was right- and failing that, decides to put him in a Cryptum. Why? Because she knows if she lets him go he will have to hunt her down, and she could never bring herself to kill him.
So, when it’s all said and done… who do you think will have the balls, so to speak, to kill the other? Because after all Cortana’s done, there’s no coming back.