Obviously there are spoilers for season eight, both actual and speculative, behind the cut. Do not read this if you do not wish to be spoilt.
Tony will not be returning in Season Nine. Yes, I know it's been said that Michael Weatherly has re-signed his contract for multiple seasons, but I think that's a red herring. I think a deal (which included being allowed to direct an episode) has been done whereby he will end his time with NCIS at the end of this season, but he'll keep quiet about it, because TPTB want to really surprise people.
Why do I think this?
Well firstly we know MW's wife hates the character Tony DiNozzo, MW has said more than once, and given how many hours he must spend each week being Tony, not to mention the fact he's admitted he'll slip into 'Tony' at the drop of a hat, it must be difficult. Or maybe MW asked for more money than TPTB were prepared to pay him?
Also, the fact is he's a seasoned agent who has been in his position for ten years now, surely by now it's time he was moved on and up? For him to have moved no further in ten years isn't good character development. However, most of my 'evidence' comes from the season so far, plus the most recent spoilers for the finale story-arc.
We know Tony knows he made a big mistake four years ago when he turned down that chance of having his own team - that has come out in two recent episodes. Plus, we have Tim telling Ziva that Tony can't turn down his own team again. Plus, we know there are going to be changes at NCIS. Plus, we suddenly have the agent who got the team after Tony turned it down popping up in DC. Now we all know TPTB play with us and mess us about and give us false information, but to bring back a subject that was dead and done four years ago now and to make such a big thing about it and to make it so clear that Tony knows he made a mistake to me screams of something more than a red herring.
In the most recent spoilers Ausiello goes out on a limb and says he thinks the serial killer 'target (and possibly take out) a member of Gibbs's team'. Now I know over on spoilersforncis it's generally thought and feared it will be Ziva as CdeP has not yet, as far as anyone knows, re-signed her contract.
However, I differ. I think the killer with take out E.J. Bartlett, the person who got Rota after Tony turned it down. I think her team will help out Team Gibbs and I think she'll be killed. Tony will be offered Rota again and as Tim said, he can't afford to turn it down again. He'll accept and thus he'll leave, I think the team will be reassigned to Rota rather than working out of the DC office.
So that's my theory. I'm probably way of base. However, I really do think something is going to come of the Rota references, the fact Tony knows he made the wrong decision and the fact he can't turn down a team for a second time.
ETA: I'm not a huge fan of change, but one way or another I do fear there will be a change to the team this season; we're due it! We lost Kate at the end of S2, three seasons later we lost Jenny, we're now another three seasons later.