The Halo Plot

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The Halo Plot:
In the distant past, a race known as the Forerunners controlled the galaxy. The Forerunners used their advanced technology to protect life, but were caught off-guard by an alien parasite known as the Flood. The Flood, which spread through infestation of sentient life, threatened and overran many worlds in the galaxy before the Forerunners could attempt to contain the threat. A group of Forerunners conceived a final solution—using an installation known as the Ark, they built seven 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 finally activated the rings and disappeared.

Thousands of years later, humanity—under the auspices of the United Nations Space Command or UNSC—have colonized many worlds thanks to the development of faster-than-light "slipstream" travel. Eventually tensions escalate between the older and more stable "Inner Colonies" and the more remote "Outer Colonies", leading to civil war. The UNSC creates an elite group of 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, together known as the Covenant. The Covenant leadership declares humanity an affront to their gods—the Forerunners—and begins to methodically exterminate humanity. The Covenant's superior ship technology proves a decisive advantage—though effective, the Spartans are too few in number to turn the tide in humanity's favor. "The Cole Protocol" is enacted to prevent the Covenant from learning the location of any other human worlds, including Earth.

In 2552, the Covenant arrive at Reach, the UNSC's last major stronghold, and bombard the planet, turning much of its surface to molten glass. The Master Chief, seemingly one of the last Spartans alive, escapes on the Pillar of Autumn. Following directives to avoid leading the Covenant to Earth, the Autumns artificial intelligence (AI) Cortana selects 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 Master Chief's help. Before the pair can activate Halo's defenses, however, Cortana reveals that Halo's activation would mean their own destruction. The Master Chief and Cortana instead detonate the Autumns engines, destroying Halo and preventing the escape of the Flood. The two and a few other human survivors return to Earth, after learning of an impending Covenant invasion of the planet.

Soon after a small Covenant fleet arrives at Earth. Most of the fleet is destroyed, but a single ship under the command of one of the Covenant's triumvirates, the Prophet of Regret, breaks through the human defenses and invades the African city of New Mombasa. Before the humans can assault Regret's carrier, he retreats through a slipspace portal, pursued by the Master Chief aboard the human ship In Amber Clad. Regret travels to another Halo installation, where the Master Chief kills Regret. Inner turmoil in the Covenant leads to civil war between the various member races. 
Learning that the activation of the Halo Array, a central tenet of the Covenant religion, would lead to their extinction, the Covenant warrior Arbiter and his Elite brethren ally with humanity to stop the rings from being fired. The aborted activation of the ring 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, who excavate a Forerunner artifact in the African desert. The artifact creates a slipspace portal leading to the Ark. The Master Chief and Arbiter travel through the portal to kill the last High Prophet, Truth, and discover the installation is building a new ring to replace the one destroyed previously. In order to destroy the spreading infestation led by the Flood intelligence Gravemind, the Master Chief activates the incomplete ring—as the Ark lies outside the Milky Way, the blast will destroy the Flood and spare the galaxy at large. 

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.