RESUME

In the distant past, an intellectual race called the Forerruners fought an alien parasite known as the Flood. The Flood, which spread through infestation of sentient life, overran much of the Milky Way Galaxy. The Forerunners conceived a weapon of last resort to combat the Flood. Using an installation known as the Ark, they built large ring-shaped megastructures known as Halos. The Halo Array, when activated, would destroy all sentient life in the galaxy—depriving the Flood of their food. Delaying as long as they could, the Forerunners activated the rings and disappeared.
Tens of thousands of years later, in the 26th century, humanity—under the auspices of the Unites Nations Space Command, or UNSC—colonize many worlds thanks to the development of faster-than-light "slipspace" travel. Tensions escalate between the older and more stable "Inner Colonies" and the remote "Outer Colonies", leading to civil war. The UNSC creates an elite group of enhanced supersoldiers, known as Spartans, to suppress the rebellion covertly. In the year 2525, the human colony of Harvest falls under attack by a theocratic alliance of alien races known as the Covenant. The Covenant leadership declares humanity heretics and an affront to their gods—the Forerunners—and begins a holy war of genocide. The Covenant's superior technology and numbers prove decisive advantages; though effective, the Spartans are too few in number to turn the tide of battle in humanity's favor.
In 2552, the Covenant arrive at Reach, the UNSC's last major stronghold beyond Earth, and launch an invasion of the planet. The last Spartans and UNSC military are unable to stop the Covenant from bombarding the surface with plasma. Following directives to avoid leading the Covenant to Earth, Cortana, the AI aboard the fleeing UNSC ship Pillar of Autumn, selects random coordinates that lead the ship to a Halo installation. The Covenant follow, damaging the Autumn and leading its crew to take the fight to the ring's surface. The Covenant accidentally release Flood imprisoned on the ring; in order to nullify the threat, the ring's AI caretaker, 343 Guilty Spark, enlists the help of the Spartan, John-117, or Master Chief. However, before the pair can activate Halo's defenses, Cortana reveals that Halo's activation would mean their own destruction. Master Chief and Cortana instead detonate the Autumn's engines, destroying Halo and preventing the escape of the Flood. They return to Earth with a few other human survivors, warning of an impending Covenant attack.
The Covenant, unaware of the destructive nature of the rings, attempt to fire another ring, Installation 05, in order to fulfill their religious prophecy, and to do so launch an attack on Earth. Helping the Chief to defend the Earth are Sergeant Avery Johnson and Commander Miranda Keyes. One race in the Covenant, the Elites, learn the truth about the rings, and join forces with humanity in order to stop the firing of the ring. Though they are successful, the unexpected shutdown of the installation triggers a fail-safe protocol, priming all the rings for firing from one location, referred to as the Ark. Still oblivious to the true nature of the rings, the Covenant high prophet of truth and the remaining loyalist Covenant proceed to head to Earth, where they believe the Ark is buried. A battle rages on Earth between human forces, the Covenant and a Flood-infected army. Eventually, the Covenant is repulsed and flees through a slipspace portal, and the Flood is purged from Earth, resulting in the devastation of Africa.
Following a message Cortana left aboard the Flood ship, the Chief, Arbiter, Elites, Johnson, Keyes and their troops follow Truth through the portal. Joining them is 343 Guilty Spark, who aids the Chief as he has no function to fulfill after the destruction of his ringworld. Traveling through the portal, the humans and Elites discover an immense artificial structure known as the Ark, far beyond the edges of the Milky Way galaxy. The Flood arrive en masse aboard High Charity, the Covenant's 'holy city', and begin infesting the installation, Johnson is captured by Truth. Gravemind, a being representing the group-mind of the Flood, actually aids Arbiter and the Chief in finding Truth, since the activation of the Ark would doom its species. They find Keyes, who had tried to mount a solo rescue, dead and Johnson being used by Truth to activate the Ark. The Chief and Arbiter stop the activation, and Arbiter kills Truth before he can be consumed by the Flood. The group then discover that the Ark is constructing a new Halo ring to replace the one the Chief destroyed. The Chief decides to activate this Halo; the ringworld would eliminate the Flood infestation on the Ark while sparing the galaxy at large from destruction. To activate the ring, the Chief rescues Cortana, who has the Activation Index of the destroyed Halo, from High Charity.
The Chief, Arbiter, and Johnson travel to Halo's control room to activate the ring. Guilty Spark explains that because the ring is not yet complete, a premature activation will destroy it and the Ark. When Johnson ignores his warning, Guilty Spark kills him to protect "his" ring. The Chief and Arbiter destroy Guilty Spark, activate the ring, and escape the ring's self-destruction on the UNSC frigate Forward Unto Dawn. However, the force of Halo's blast causes the slipspace portal to collapse, resulting in only the front half of Forward Unto Dawn, carrying the Arbiter, making it back to Earth. Believing the Chief to have perished, a memorial service is held on Earth for the fallen heroes of the Human-Covenant war. After the memorial service, the Arbiter and his Elite brethren departs for their home planet. But it is shown that the rear half of Forward Unto Down is floating in space, with the Chief and Cortana on board. Cortana activates a distress beacon and the Chief goes into hibernation.
The story is continued in halo4, with the Master Chief and Cortana waking four years after the destruction of the Ark, arriving on the artificial Forerunner planet of Requiem, where a human colonizing ship has apparently crashed and a splinter group of Covenant are searching for a hibernating Forerunner.