Halo is set several centuries in the future. After the development of the "Shaw-Fujikawa Translight Engine", the United Nations Space Command (UNSC) begins a program of interstellar travel and planetary colonization. Over 800 planets are colonized in 200 years, categorized as "Inner Colonies" and "Outer Colonies". The Inner Colonies, being closer to Earth, are more developed and politically stable. Due to the older planets' need for the raw materials and supplies the Outer Colonies provide, tensions and outright civil war foments between the colonies and the UNSC. The UNSC creates the SPARTAN-II Project in order to covertly suppress these rebellions. Twenty-seven years before the events of the main game trilogy, UNSC communication with the colony Harvest is lost, and the ship sent to investigate is destroyed by the Covenant, a theocratic collective of aliens bent on exterminating humanity. The Covenant leadership has declared humanity to be an affront to their Gods, the Forerunner. By 2535, almost all of the Outer Colonies have been destroyed by the Covenant; in response, the UNSC vigorously enforces the "Cole Protocol", destroying material and ships that might lead the Covenant to Earth. The Covenant possesses a significant technological advantage, and proves nearly impossible for the UNSC to defeat in space engagements. These events are only alluded to in the video games, but their full descriptions are outlined in the novels Halo: The Fall of Reach and Contact Harvest, as well as in the real-time strategy game Halo Wars.
The story arc of the game trilogy begins with the game Halo: Combat Evolved, set in 2552. The Covenant arrive at Reach, which is the UNSC's last colonial major stronghold; they vitrify the planet, leaving very few survivors. The Master Chief, the last SPARTAN thought alive, escapes on the ship Pillar of Autumn. The Pillar of Autumn, in order to avoid leading the Covenant to Earth, proceeds to coordinates selected by the female A.I. Cortana; dropping out of slipspace, the Autumn discovers the titular Halo, and is attacked by the Covenant. Battle damage forces the Autumn to the surface of the ring, where the Flood, a parasitic alien species, are accidentally released by the Covenant. The release of the Flood prompts the ring's caretaker, 343 Guilty Spark, to convince the Master Chief to activate Halo's defenses, so that the Flood can be destroyed. The Forerunners created Halo to starve the Flood of their food—sentient life—by exterminating all possible vectors for thousands of light-years in every direction. Upon discovering Halo's purpose, the Master Chief detonates the fusion reactors in the crashed Pillar of Autumn, destroying the ring; he and Cortana then escape in a fighter spacecraft.
In Halo: First Strike, the Master Chief returns to Reach, located in the Epsilon Eridani system, and rejoins the survivors of the vitrification. He and other SPARTAN-II's attack a Covenant space station, where a fleet is massing to attack Earth. The space station is destroyed, giving the humans time to prepare for the invasion. Soon after in Halo 2 a small Covenant fleet arrives at Earth. Badly beaten by the humans, the Covenant commander, the High Prophet of Regret, flees to another Halo, Installation 05, unwittingly taking the human ship In Amber Clad with him. At Installation 05, the Master Chief kills the High Prophet, leading to the replacement of the Covenant Elites with the Brutes as the preferred soldiers of the Covenant. This changing of the guard causes a schism within the Covenant. The Elites, realizing they have been betrayed, ally with the humans. The Elite warrior known as the Arbiter joins the humans Miranda Keyes and Sergeant Johnson in stopping the activation of Halo. This act inadvertently puts all the Halo installations on standby: the remaining rings can be activated remotely from a location known as "The Ark".
The Master Chief stows away on a Forerunner vessel headed to Earth, in the midst of a full-scale invasion by the Covenant. In Halo 3, the Covenant excavate a Forerunner artifact in the African desert; despite the efforts of the Elites and humans, the High Prophet of Truth activates the artifact, which opens a slipspace portal to the Ark. The Master Chief and the Arbiter travel through the portal and kill Truth; They then activate a new Halo ring under construction in an effort to destroy the local Flood, led by the intelligence known as the Gravemind, while sparing the rest of the galaxy. Because the ring's construction is incomplete, the resulting pulse destroys the ring and damages the Ark. The Arbiter escapes the explosion, but the Master Chief and Cortana are left drifting in space, trapped in the severed rear half of their ship. The Master Chief cryonically freezes himself as he and Cortana wait for rescue. In a bonus ending, the ship is seen drifting towards a mysterious planet.
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