After learning the Truth about the Halo, the Chief and Cortana decide the only thing to do is destroy it before it's activated by someone or the Flood figure out a way to get off of it.
Now Chief is fighting The Covenant, the Flood, and the A.I. Guilty Spark and his robot drones. He sneaks onto a damaged Covenant ship that the Flood are trying to escape in and retrieves the Personal Data Transmitter (PDT) from Captain Keyes' badly deformed body. Keyes' PDT is the key the duo needs to authorize the self-destruct sequence on the crashed Pillar of Autumn. The subsequent explosion caused by the PoA's reactors will destroy the Halo and everyone on it.
The Chief and Cortana make their way to the PoA crash site and fight corridor-to-corridor to get to the reactor chamber. They start the self-destruct sequence, and, as the ship explodes around them, they narrowly escape annihilation by hopping aboard a Marine starfighter docked in the PoA's hanger.
As the Halo explodes in space, Cortana scans for life in the surrounding area. No Marines, no Covenant, no Flood -- nothing but "dust and echoes." Just as before, there are no survivors but the Chief. The chief now must make his way back to Earth. As the Chief and Cortana speed away, Guilty Spark flies away into space unnoticed muttering to himself...
Source: Halo novels The Fall of Reach and The Flood