By the power of truth, I, while living, have conquered the universe.
The Flood are of 'extra-galactic' origin, no doubt that many are trapped on the other Halo Rings in containment facilities, but due to the weather conditions of the Halos -made to test the Flood organism's limits- I'd imagine that they're rather stuck.
The Covenant are not all dead, there are still those who did not go through the Portal and those who reside on their homeworlds. Depending on the actions of the Humans and Elites after the war, they're not much of a threat.
The Grunts tend to side with those they believe to be strongest, probably some will try to switch to the Human/Elite side and some will remain by the Brutes. Jackals are simply pirates and will probably stay clear of the Covenant, along with the Drones, Hunters and Engineers.
The Prophets are near-extinction, the population dwindles around 1000, so they could be considered an effective minority.
There will probably be some uprisings but they'll be easily quelled by the Humans and Elites who would presumably try to rebuild what they've lost.