This page is largely incomplete; I will later feature summaries of the ingame action in Halo as well as its continuation in Halo: First Strike by Eric Nylund, and possibly story speculation on the Forerunners, Flood and Covenant. The below information is a summary of that found in Halo: The Fall of Reach, also by Nylund.

It is the year 2552. Humankind has been pushed to the brink of extinction by the deadly fellowship of alien warriors known as the Covenant. Thirty-two years of war has resulted in nothing but loss after loss for the humans, and the scientific community is convinced that the human race will be exterminated in a matter of months, perhaps as long as a year. After a hostile first contact, the Covenant, with superior technology and numbers, proceeded to wipe out several human-held planets using a brutally destructive tactic. They would attack a planet in great force, sending ground troops to capture and hold the surface. After they either eliminated everyone on the surface or were eliminated themselves, the ships in space proceeded to bombard the planet with plasma in a technique known as "glassing". Glassing was utterly devastating, often leaving little more than crystallized carbon of the planet's surface, and due to the overwhelming power of the Covenant ships, there was little human forces could do to stop them. 

Humankind has one remaining source of hope. A number of years ago, the military unveiled Project: SPARTAN II. The goal of the project was to create several specialized combat units, essentially super soldiers. Upon first contact with the Covenant, the SPARTAN II project took on newfound importance. Under the leadership of Master Chief John 117, the SPARTANs, equipped with powerful MJOLNIR Mark V armor, won several major victories against the Covenant ground forces. While the SPARTANs can do little against Covenant warships, they were once able to infiltrate and destroy a small Covenant vessel.

Hoping the team would be able to once again board a Covenant vessel, Dr. Halsey, creator of the SPARTAN program, assigned a new mission. They were to board a Covenant vessel, and, with the help of new augmentations, including an enhanced starship grade artificial intelligence known as Cortana, capture it and take it back to Covenant space. Once there, their mission was to capture a Covenant leader and bring him back to human space. Captain Jacob Keyes and his new vessel, the Pillar of Autumn, were to disable the vessel for capture and provide backup for the mission.

However, things went awry. The Covenant attacked Reach, one of the most important planets in the human network of colonies. As well as being a shipyard, Reach was a major hub of military and scientific activity, and the birthplace of the SPARTAN II project. Furthermore, it was one of the closest colonies to Earth. Fearing the Covenant would move from there to Earth, Fleet Command recalled all available ships, including the Pillar of Autumn, to defend Reach. 

The humans had one major advantage: twenty Heavy Orbital Magnetic Acceleration Cannons, or Super MACs. MACs, or Gauss cannons, are capable of launching a projectile between twenty and fifty tons across space at a rate of 2/3 of the speed of light. The effect is devastating. However, the cannons had a vulnerability: the reactor complex that serviced them was on the surface of Reach. Somehow, the Covenant learned of this vulnerability and went after the reactors.

Another critical vulnerability was discovered. A small cruiser owned by the Office of Naval Intelligence, docked in the Reach Orbital Docking Facility, contained an intact navigational database which held the location of Earth. In order to deal with both threats to security, the majority of the Spartan team went to assist the Marines defending the reactor complex groundside, while the Master Chief and two of his most trusted soldiers went after the nav database. 

While the Master Chief was successful in his mission, he was the only survivor of his group, and the reactor complex fell. The entire group of Spartans on the surface was subsequently presumed dead in the Covenant glassing of the planet. (As we have now learned, a number of that assault group survived and later were found by the Master Chief; though many Spartans died in a later battle, several still survive: John, Kelly, Linda, Fred and Will.) With the fleet in disarray, the battle-scarred Pillar of Autumn, with the Master Chief on board, went to Slipspace on an apparently random vector.

However, the heading was not as random as some would assume. Cortana, who had been assigned control of the Pillar of Autumn, had been analyzing a crystal artifact recovered from the Covenant, and suddenly realized it contained Slipspace coordinates. It was to these coordinates the Pillar of Autumn jumped.

Introduction
Backstory