The year is 2552 AD. 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, has pushed the colonization effort forward; billions of humans now live on habitable planets in other solar systems. A keystone of humanity's colonization program 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 the sudden stop of broadcast signals and communications 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 the battlegroup.

This was humankind's first encounter with a group of aliens they eventually came to know as the Covenant, a collection of various alien races united in their fanatical religious devotion. Covenant religious elders declared humanity an affront to all the Gods, and it was Their will that the Covenant destroy the human race. The Covenant warrior castes waged a holy war upon humanity with gruesome diligence and ruthlessness.

After a series of crushing defeats and obliterated colonies, 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, colonized planets, and any human settlements. Make randomized Slipspace jumps without proper navigational calculations, if the need arises. Vessels in danger of capture must purge their navigational databases and records and self-destruct. If the Cole Protocol is not carried out by a ship in danger from the Covenant, it is deemed an act of treason and punished by execution or life-imprisonment.

On Reach, a secret military project to create cyborg super-soldiers takes on newfound importance and is rushed forward with all speed. The soldiers of the SPARTAN-II project rack up an impressive record against the Covenant, 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-II's and learn the location of the Covenant home world. They will fly to the planet disguised in the Covenant ship and capture the leadership caste, bringing them back to UNSC controlled space, to force a peace agreement. 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 surviving SPARTAN-II and make a blind jump into deep space, hoping to lead the Covenant away from Earth.