From the Manual:

The year is 2552 (read Halo: The Fall of Reach for past infomation). Planet Earth still exists, but overpopulation has forced many of her former residents to colonize other worlds. Faster-than-light travel is now a reality, and Earth's unified government, through the United Nations Space Command (UNSC), has put its full weight behind the colonization effort; millions of humans now live on habitable planets in other solar systems. A keystone of humanity's colonization efforts is the planet Reach, an interstellar naval yard that builds colony ships for civilians and warships for the UNSC's armed forces. Conveniently close to Earth, Reach is also a hub of scientific and military activity.

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 efforlessly 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 rank up an impresive record against the Covenant in test deployments, but there are too few of them to turn the tide of the war.

Exhisting 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.