Will the UNSC itself and ONI in particular become an outright antagonist as the Halo saga goes on? Spartan Ops has seen Halsey alienated and betrayed to the point where she's seems willing to side with the Storm for revenge. We've seen the UNSC carry out increasingly ruthless, unethical actions as the series has unfolded and glimpses of its citizens living under an almost Orwellian surveillance state.
ONI is out of control, plain and simple, and has been for quite some time, operating with little in the way of accountability or oversight. Citizens are routinely lied to and misinformed, and people on Earth were essentially living in a fantasy world of propaganda until the moment the Covenant finally found it and struck. Any sort of reform or seperatist movements are infiltrated and harshly suppressed by ONI and the military.
Has the time come for Halsey and the last of her Spartans, who were taken as children to protect humanity, to save humanity from the tyranny of the UNSC?
Save what's left of humanity from the people who won the war? And Halsey isn't exactly a saint, unless kidnapping a Spartan in 2552 shortly before the enemy finds the homeworld then later luring away three more after that has happened are good things to you. (see First Strike and Ghosts of Onyx) Not that she was even a saint before that.
ONI has been doing the same thing they've been doing for over 40 years at least by now. The UNSC at large is not to blame, and lets face it, a revolution against the UNSC when they only had 30 spartans didn't really get anywhere did it? Now try it against hundreds, all with years of combat experience fighting aliens far more capable than anything human rebels could muster.
And at this point, if a planet goes rebel, the Infinity just needs to come in, drop all its spartans on the ground, and the planet would surrender without a shot being fired.