Depending on what the writers are going for, I predict that Booth will not show to their meeting place, and we will quickly discover that he is MIA or some such in Afghanistan and the remains of whoever he was working with will be found, and then the first few episodes will focus on trying to find him and get him back. If that doesn't happen, it'll be Bones who doesn't show, who turns up missing, and they whole song and dance will be done in effort to find her instead.
That is if the writers decide to do the cliche thing (one of these days I will learn how to type that dash-accent thingy over the 'e'); if they don't go with the cliches for once (and I was impressed that there weren't any proposals of undying love or some sort of desperate kiss in the goodbye scene at the airport for the season finale, so you never know), it will probably be some weird, hopeless case that they can't figure out; a serial killer or something so the only way to stop it is to call Brennan back in because she is the Best of the Best, and Booth might be dragged back for the same reason.
So, yeah, that is what I am predicting. Or speculating on. Or whatever. Will see how motivated I am in September to see if I was right.