After the fiasco with the second Halo ring, Master Chief ends up crash landing on Earth where another Covenant leader, the High Prophet of Truth, manages to open a slip-space portal to the Ark, the control center for the Halo-array and location of Cortana.
The Chief and Arbitor manage to kill the Prophet of Truth with the help of the Flood Gravemind before Truth is able to set off the Halo rings. But Gravemind betrays them when the deed is done.
As they escape the Flood, the heroes discover that the Ark was building a replacement Halo ring to which they decide to prematurely activate to destroy the ring, the Ark and the Flood all with one stone. When they succeed, Master Chief, the Arbiter and Cortana escape in the UNSC ship Forward Unto Dawn, but it gets cut in half by an unstable slip-space portal. The Arbiter crash lands on Earth and Cortana and Master Chief are left floating through unknown space, setting us up neatly for the events of Halo 4.