Four years after the events of Halo 3, Forward Unto Dawn drifts towards Requiem from the destroyed ring. Cortana wakes Master Chief from cryonic sleep shortly before rogue Covenant forces board the vessel. The remnants of Forward Unto Dawn are caught in Requiem's gravity well and pass through an opening to crash-land on its interior. As Chief and Cortana explore Requiem, fighting hostile Covenant and Prometheans, Cortana malfunctions. She reveals that she is experiencing "rampancy", a declining mental state where AIs past their operating expectancies "think" themselves to death. Chief promises to get Cortana to Earth, believing that Cortana's creator, Doctor Catherine Halsey, can fix Cortana's condition. Chief and Cortana pick up garbled transmissions from a human ship, Infinity, who have picked up Dawn '​s distress call. Cortana attempts to warn Infinity away from Requiem's gravity well and directs the Chief to deactivate what she believes are communications jammers. Instead, the Chief releases the Didact, an ancient Forerunner warrior, from imprisonment. The Didact takes control of the Prometheans and Covenant and attacks Infinity after it is dragged into Requiem.

Chief makes contact with Infinity and helps repel the Didact's attack. Chief and Cortana recommend attacking the Didact while he is vulnerable, but Infinity captain Del Rio orders them to destroy the gravity well so their ship can escape. In the process, Chief is contacted by a Forerunner known as the Librarian – the wife of the Didact, as well as ancient humanity's protector. She explains that the Forerunners were divided on how best to combat the Flood. After failing to discover a way to immunize biological beings from the parasite, the Didact used a device called the Composer to convert the warriors under his command into digital versions immune to infection. Requiring more soldiers, the Didact forcibly converted captured humans into Prometheans, before being stopped and imprisoned by the Librarian. The Librarian, who has guided humanity's development, accelerates the Chief's evolution; this grants him immunity to the Composer.

After destroying the gravity well, Del Rio orders a retreat back to Earth, doubting the Chief and Cortana's testimony. The Master Chief disobeys orders to stand down and relinquish the malfunctioning Cortana, and stays behind to oppose the Didact. Infinity executive officer Commander Lasky gives Chief an armed transport and wishes him luck. Chief and Cortana attempt to sabotage the Didact's ship before he leaves, but when they are unsuccessful they follow the Didact to a Halo ring, Installation 03. The Composer has been moved from the ring onto the nearby Ivanoff Research Station, which the Covenant attack. The Chief defends Ivanoff, but the Didact retrieves the Composer and uses it on the station, composing every individual except the Chief.

Chief and Cortana use a fighter to follow the Didact's ship through slipspace towards Earth. Aided by Infinity, now commanded by Lasky, and the UNSC home fleet, the Chief boards the Didact's ship with a nuclear warhead. Cortana inserts copies of herself into the Didact's computer systems to overwhelm the Didact's shield, but not before the Didact directs the Composer at Earth. With the help of Cortana, the Chief defeats the Didact, who falls into a slipspace corridor generated underneath the Composer. The Master Chief activates the bomb but is saved by Cortana, who sacrifices herself. The Chief is found by a UNSC rescue team and is taken back to Infinity, where he, mourning the loss of Cortana, talks with Lasky about Earth, duty, and what his duty as a soldier means.

In a post-credits cutscene, UNSC forces descend on the city of New Phoenix, the location the Didact used the Composer on, to find its inhabitants composed. In a narration, the Didact proclaims the Forerunner's role as custodians of the galaxy having to bear the Mantle of Responsibility, and humanity as the greatest threat in the galaxy. Master Chief removes his armor aboard Infinity; if the player completes the game on Legendary difficulty, the Chief's eyes are briefly shown.