The ring known as a Halo has been successfully destroyed but not without the cost of many lives. The remaining Marines and Master Chief successfully made it off the ring world and made it back to earths main fleet. Following a ceremony honoring the dead, the Covenant stage a high stakes attack on the fleet and Earth. Springing into action, Master Chief helps repel the Covenant forces and follows them, finding himself at another Halo ring. At the same time, the Covenant ranks are slowly begging to see strife. The Elite class, who always saw favor among the Prophets has been downcast in favor of the Brutes. A civil war is slowly brewing between the classes and leading the rebellion is the Arbiter, a once loyal member of the Prophets guards who has begun to question his beliefs.

Little do either know, the coming battle against the dreaded Flood and the remaining Covenant forces will force Master Chief and the Arbiter to work as equals. The danger is high, the outcome is slim and the fate of the entire universe rests in the hands of the last Spartan and an alien heretic...