So we know ONI has a huge lust for power, and this thing is powerful. They could have sent the UNSC to go obtain this at all costs. Master Chief on the other hand comes in contact with the Didact and finds out why no one should use the mystery thing. Chief tries to convince the UNSC but at some point they ultimately fail.
So maybe at a point in the game we will be fighting Covenant, fighting forerunner to stop them from killing humans, and fighting humans because the UNSC needs the MC out of the way.
The biggest problem though is that many humans view Master Chief as a huge hero, but maybe in 2257 (or is it 6?) the UNSC has seen that Spartan II's have run their course and Spartan IV's are the way to go. Or when Parangosky reveals the secrets behind the Spartan II program all respect for them will be lost.
This would also really play some mind games with him and cause inner conflict which would add to his personality, which is something 343 wants to do.