The Plot of Halo 3

The only plot points that have been revealed so far are that Master Chief is back on a thoroughly conquered and Covenant controlled Earth. Cortana is still a prisoner of Gravemind, Covenant ships are hovering over an excavation site only a few miles from the ruins of New Mombasa, The Covenant have also uncovered a large artifact in this site, which is largely believed to be The Ark. The Arbiter, along with the remaining Elites, have allied themselves with the human forces, according to the Halo 3 Website