In December 2559, the UNSC ship Infinity arrives at Halo Installation 07. Upon arrival, the ship is ambushed by several dreadnoughts that are operated by the Banished. While defending the ship's hangar bay from multiple raiding parties, the Master Chief is caught off-guard by Atriox, the leader of the Banished, and is subsequently defeated in a one-on-one duel. Atriox throws the Chief from the edge of the hangar bay, leaving him stranded in space.

Six months later, a UNSC pilot recovers the Chief adrift in space. While the Pilot wants to flee, Master Chief insists on continuing the fight against the Banished. The Chief and Pilot travel to Zeta Halo, which has been severely damaged by an unknown calamity. On the ring, Master Chief locates the Weapon, an AI designed to imitate Cortana in order to capture her for deletion. While the Weapon states that she was successful in her mission, she has failed to self-delete as per her directives. Master Chief retrieves the Weapon, and experiences visions of Cortana's memories and thoughts left as residual data.

Zeta Halo is controlled by the Banished, now led by Atriox's lieutenant Escharum after Atriox's apparent death. The dying Brute is invigorated to have Master Chief as his final opponent. Master Chief, the Weapon, and a reluctant Pilot rally scattered UNSC forces on the ring's surface, while looking for any Spartans that haven't been picked off by The Hand of Atriox, Escharum's team of Spartan killers. Inside the Forerunner installation known as the Conservatory, Master Chief encounters Despondent Pyre, the AI caretaker of Zeta Halo. Despondent Pyre attempts to warn Master Chief of a threat contained on the installation, but is destroyed by the Harbinger, an alien awoken by the Banished. The Harbinger claims that her people, the Endless, were imprisoned by the Forerunners on Zeta Halo. She has allied herself with the Banished in order to rebuild the Silent Auditorium, a facility that will allow her to free her people. The Banished, in turn, will use the repaired Halo as a weapon against humanity.

Master Chief defends the Pilot from a duo of Spartan killers deployed by Escharum. The Pilot reveals that he was a civilian engineer aboard Infinity who stole a Pelican to flee the battle. The Chief comforts him, admitting his own guilt over his failure to save Cortana. Master Chief and the Weapon stop Zeta Halo's repair process by disabling a series of spires on the ring, but are unable to stop a section of the Auditorium from being rebuilt. When the Harbinger attempts to hack the Weapon, the Chief activates a failsafe to delete the AI. The Weapon repels the Harbinger and deactivates the failsafe, angrily asking why Master Chief does not trust her. After seeing a vision in which Cortana uses the Guardians to destroy the Brutes' home planet of Doisac, the Weapon realizes that she is a copy of Cortana, and insists that Master Chief delete her so she does not become like her predecessor; Master Chief refuses, stating that he wants to trust her. The Pilot is captured by Jega 'Rdomnai, an Elite Spartan killer and a close friend of Escharum, as bait for Master Chief. Unwilling to let the Pilot die, Master Chief infiltrates the Banished facility and saves him, defeating Jega 'Rdomnai and Escharum in the process.

Master Chief and the Weapon rush to the Auditorium to stop the Harbinger. The two learn that Cortana was captured by Atriox after the Weapon locked her down; upon realizing that Atriox intended to access the ring's secrets, Cortana destroyed herself, damaged Zeta Halo, and prevented the Weapon from being deleted. In a recorded message, Cortana says goodbye to the Chief and encourages him to work with the Weapon. The Chief defeats the Harbinger, but is unable to stop her from contacting someone regarding the Endless. Afterwards, the Weapon and Chief reunite with the Pilot, who reveals his name is Fernando Esparza. The Weapon decides to choose a name for herself.

In a post-credits scene, the surviving Atriox uses a key to unlock a sealed door, leading to the Endless. If the game is finished on Legendary difficulty, the scene features dialogue between Despondent Pyre and a Forerunner official about the imprisonment of the Endless. When Despondent Pyre states that she cannot oversee the study of the Endless alone, the Forerunner replies that the AI Offensive Bias has been deployed to assist her.

Hours played: 33h 35m

Achievements: 51/144

Completion: 35%

Gamerscore: 595/2020