Thirty-two years ago, contact with the outer colony Harvest was lost. A battlegroup sent to investigate was almost completely destroyed; only one badly damaged ship returned to Reach. Its crew told of a seemingly unstoppable alien warship that had effortlessly annihilated their forces.

This was humankind's first encounter with a group of aliens they eventually came to know as the Covenant, a collective of alien races united in their fanatical religious devotion. Covenant religious elders declared humanity an affront to the gods, and the Covenant warrior caste waged a holy war upon humanity with gruesome diligence.

After a series of crushing defeats and obliterated colonies, UNSC Admiral Preston Cole established the Cole Protocol: no vessel may inadvertently lead the Covenant to Earth. When forced to withdraw, ships must avoid Earth-bound vectors -- even if that means jumping without proper navigational calculations. Vessels in danger of capture must self-destruct.

On Reach, a secret military project to create cyborg super-soldiers takes on newfound importance. The soldiers of the SPARTAN-II project rack up an impressive record against the Covenant in test deployments, but there are too few of them to turn the tide of the war.

Existing SPARTAN-II soldiers are recalled to Reach for further augmentation. The plan: board a Covenant vessel with the improved SPARTAN-IIs and learn the location of the Covenant home world. Two days before the mission begins, Covenant forces strike Reach and annihilate the colony. The Covenant are now on Earth's doorstep. One ship, the Pillar of Autumn, escapes with the last SPARTAN-II and makes a blind jump into deep space, hoping to lead the Covenant away from Earth.