Halo: Combat Evolved begins with the UNSC Pillar of Autumn emerging out of slipspace after the Fall of Reach, only to find a huge ring world—a "Halo"—floating in space. Master Chief Petty Officer John-117, a SPARTAN-II, is aboard the Pillar of Autumn when the ship comes under attack by the Covenant, a religious alliance of aliens and the archenemy of humanity.

With the ship about to be overrun, Captain Jacob Keyes, the commander of the Autumn, orders John-117 to protect the ship's artificial intelligence, Cortana. She carries highly sensitive information about the United Nations Space Command, including the location of Earth, which would prove disastrous if captured by the Covenant. John-117 evacuates the doomed ship for the surface of Halo to protect Cortana. With the UNSC Marines by his side, Cortana providing direction, and his assault rifle ready and loaded, John-117 sets out to uncover the mysteries of Halo and fight the Covenant.
After meeting up with surviving UNSC forces under Staff Sergeant Avery Johnson, John-117 participates in a mission to rescue Captain Keyes from the Covenant cruiser Truth and Reconciliation. After rescuing the Captain, Cortana learns that Halo appears to be a weapon that holds great religious significance to the Covenant. Realizing that the Covenant cannot be allowed to control Halo, Keyes dispatches John-117 to secure Halo's control room while he leaves with Johnson to secure a Covenant weapons cache.
With UNSC Marines as support, John-117 leads an assault on the Silent Cartographer, a map room which holds information on every location on the ring, including the control room. Heading to the ring's control room, Cortana is inserted into the ring's computer system and learns that Halo was made by the Forerunners, an ancient alien race that the Covenant worship as gods. However, Cortana soon learns that there is something else on Halo, something that terrifies the Covenant. Frightened, she says that John has to stop Keyes from accessing the "weapons cache" before it is too late. John-117 leaves for the last spot where Captain Keyes and Sergeant Johnson's squad were seen, an underground facility in a swamp. He finds evidence of battle all over the facility, and soon finds a recording of one Marine, which details Keyes' squad encountering a new threat: the Flood.
The Flood is a parasitic species which received their name due to the way they assimilate all resistance with overwhelming numbers. Free for the first time in a hundred thousand years, the Flood sweeps across Halo, devastating Human and Covenant forces alike. The release of the Flood prompts 343 Guilty Spark, the eccentric AI Monitor of the ring, to activate Halo's defense systems. The AI instructs the SPARTAN-II to activate Halo by obtaining the Activation Index from the Installation's Library. The Chief does so, battling hordes of Flood along the way, and returns to the control room. Before Halo initiates its systems, Cortana intervenes and tells John the truth about the Forerunner structure and its purpose- Halo was designed to eliminate the Flood threat by starving the Flood of any life source large enough to sustain them; when fired, it would essentially wipe out all sentient life in the galaxy. Realizing the threat of Halo, Cortana instructs John-117 to detonate the Autumn's fusion reactor. This detonation would result in the destruction of Halo, which was against 343 Guilty Spark's protocol.
Before doing so, the two sabotage three generators needed to power Halo, which buys them enough time to locate Captain Keyes, now succumbed to the Flood, and steal his neural implants to operate the Autumn. After battling his way through scattered and disorganized Covenant forces, the spreading Flood, and the Sentinels under direct command of 343 Guilty Spark, John-117 successfully overloads the ship's engine, and he and Cortana evacuate from Halo in a Longsword before the Autumn's engine detonates and destroys Halo. The pair appear to be the only survivors, and John-117 realizes that they are simply beginning a harrowing battle.
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