Another idea that I have is to have the Flood consume a colony world. Either the Rebels stole one of the bioweapons CrimsonVolver mentioned and accidentally release the parasite or the Storm Covenant accidentally release the parasite on one of Sanghelios' moons. There could be a cutscene similar to the one at the beginning of Halo 4 where the covenant are laying waste to civilians . It would show the Flood brutally infecting civilians and terraforming the planet's surface and atmosphere. It would have the Chief trying to activate a NOVA bomb because the Flood have control of AA gun to shoot down would-be glassing or orbital bombardment ships, and that they have access to off world transportation. As the Chief progresses he sees survivors getting overwhelmed and biomass forming. Chief would activate the bomb and then try to get off world in a Broadsword. But between him and the ship stands a Juggernaut and a boss battle ensues. It would play out similar to The Maw in CE but it wouldn't be the final mission.