Alright, don't troll me on this, but here's my theory on what might happen in Halo 4.
Cortana is still in the Pillar of Autumn during the start, as Masterchief did not pick her up as he was afraid of possible corruption. Anyway, Masterchief wakes up to find himself on a desolate forerunner abandoned planet full of flood, but unlike the previous flood incarnations, it has adapted to be more stealthy and leave little trace as it was created by the Gravemind during the great Forerunner/Flood war, to infiltrate the planet and take it over.
However, masterchief does not encounter them as he travels. Anyway, he walks up to a control panel and just before he activates what seems like a harmless switch, he hears a noise. He turns around with his gun pointed, but he can't see the stealthy flood infection form that made the noise, and turns back around slightly more wary. He activates the switch and the ground shakes, with a beam of light shooting upwards, moving clouds and changing the sky. It creates a slipspace portal (unbeknownst to the chief) to Earth, as this planet *spoilers* was meant to be a way of escape from the Halo rings for the Librarian, made by the Didact, to save her. *spoiler*.
Two ships come through, one a Unsc Frigate, and the other one a strange black corvetter, seemingly alien. It seems that in the time 117 has been gone, the elites have allied with the UNSC, and changed the colour of all of their ships (in return for the exchange of weapons e.g. MACs, Plasma torpedoes, glassing beams, that sort of stuff) and green phantoms, and green pelicans investigate and are overjoyed to find the chief. The phantoms take back the Chief and any other relevant items (not cortana as she has hidden herself because *spoiler* she has come to the conclusion that the flood is the only soultion to end war *spoiler* ) while being slightly confused about not finding her,to the Rejoice of Salvation, and the UNSC ship (the Dove, definitely a frigate) stays to investigate. Chief gets taken through the slipspace portal, while an ancient parasite plots.
Okay, so what do you think? Please make any canonical corrections, like if Elite ships can't be black, and say what you think. I'll continue soon.
[Edited on 11.27.2010 3:55 PM PST]