Reach takes place on the UNSC fortress world of Reach during the weeks prior to Halo: Combat Evolved. Noble Team, a squad of Spartan supersoldiers, is ordered by Colonel Urban Holland to investigate the sudden loss of transmission from the Visegrád Relay Communications Outpost. Expecting Insurrectionists, the team is baffled to discover that it is the work of the Covenant, and an invasion becomes apparent. As the Covenant begin their assault on the planet, the UNSC begin their heroic yet hopeless attempt to halt the brutal alien invaders. Soon after, Noble Team is deployed to "Sword Base", an installation belonging to the Office of Naval Intelligence (ONI), for defensive purposes. Dr. Catherine Halsey, mastermind of the SPARTAN-II Program and the MJOLNIR Powered Assault Armor worn by all SPARTAN characters, informs Noble Team that the Covenant at the relay were searching for important information pertaining to the Covenant religion.
As the Covenant arrive on the planet in force, Noble Team is dispatched on various defensive missions such as assaulting a Covenant ground base and removing fortified Covenant defenses. One of these defenses was a Spire transporting Covenant forces onto Reach. Noble Five's (Jorge) and Noble Six's mission was to take down the shields protecting the Spire. After Noble Six brought down the shield of the Spire, the frigate UNSC Grafton destroys the Spire with MAC Rounds. When a massive supercarrier joins the fight and destroys UNSC Grafton, Kat comes up with a plan to strike back at the Covenant. Her idea is to sneak a Slipspace Bomb onto the Ardent Prayer which they would then send on a refueling run to the supercarrier to activate the bomb. Six infiltrates the Corvette, while Jorge got the pelican to dock with the supercarrier and then detonate a makeshift slipspace bomb, but the detonator malfunctions, Jorge sacrifices himself to destroy the carrier; soon thereafter a larger Covenant fleet arrives to continue the assault. Six is thrown out of the corvette by Jorge to fall back unto the planet Reach. Six lands near New Alexandria, which is already besieged by the Covenant. Noble Six regroups with the rest of the team in assisting with the evacuation of the planet. Then, Noble Six was assigned to destroy covenant jammers in the skyscrapers of New Alexandria. During their escape, Kat is killed by a sniper and New Alexandria is glassed by the Covenant.
Colonel Urban Holland recalled Noble Team to Sword Base to destroy the data that the Covenant are looking for underneath the base, along with the artifacts the Covenant want to get their hands on. They soon meet Halsey and she shows them an ancient Forerunner artifact that she believes is key to winning the war. The artifact is an AI named Cortana, and she choose Noble Six to carry her to safety. Noble Six, Carter, and Emile are entrusted with the task of transporting the artificial intelligence, Cortana, and the information she carries, to the UNSC Pillar of Autumn. Meanwhile, Jun is assigned to evacuate Halsey in a Pelican dropship. Charges are detonated in the artifact, ultimately destroying it and any evidence of its information.
During the journey to the Pillar of Autumn's dry dock, Carter is hit by Banshee fire and is mortally wounded. Six and Emile jump out of the Pelican and slide down to safety. After they fight out of many caves, they encounter a Scarab, which attempts to kill the Spartans. Carter sacrifices himself and the team's Pelican to destroy the mobile assault platform. Finally, Six and Emile reach the ship breaking yards. Emile takes control of a MAC cannon to defend the Autumn while Captain Jacob Keyes arrives to receive Cortana from Noble Six. Emile is slain by Elite Zealots, and Six opts to remain on Reach and take Emile's place at the gun while the Autumn escapes. The game depicts the opening scene of Halo: Combat Evolved, in which Cortana discovers Installation 04, followed by the credits and a personal message of thanks from Bungie.
The post-credits scene puts the player in control of Noble Six's last stand against overwhelming Covenant forces. After sustaining more and more damage, Six's helmet cracks. Six eventually casts aside the helmet and is eventually overwhelmed by a group of Sangheili. Six's shattered helmet is left discarded on the ground in a shot that mirrors the game's opening scene. Over thirty years later, the same helmet rests on the grassy plains of a now-rejuvenated Reach. Life has returned, and recolonization has begun. A narration by Halsey eulogizes Noble Team's sacrifice, which enabled the victory over the Covenant.