So I thinks I gots it! Master Chief crashes onto a covenant controlled Reach BUT before he does he crashes into a Forerunner ship ( and destroys it ). So, he thinks the covenant control Reach but finds out Noble Six kills himself in order to stop the Covenant threat. Suddenly, he finds a distress signal from a long time ago after Six dies, explaining before the Covenant were defeated the Flood crashed into the planet, including the remains from High Charity and the Halo seen in Halo 3's last level. Realising the Prophets body is on the ship, the Flood infect him, giving him a massive overdose and transforming him into the picture here in the URL or go to google, type Halo 4, choose the first one. The events after I haven't figured out yet. Guys, really don't give me grief over this one, its just what I think.