Synopsis

It begins with the trial and punishment of the former Supreme Commander of the Fleet of Particular Justice, Commander Thel 'Vadamee, later on to be the future arbiter, who is branded with the Mark of Shame by Tartarus due to his failure to protect the Sacred Ring during the events of Halo: Combat Evolved.

The story then turns to Earth's Orbital Defense Platform Cairo Station, where the Master Chief receives the new MJOLNIR Mark VI armor. He then meets Admiral Terrence Hood for an award ceremony held for the dual purposes of awarding meritorious acts and boosting the morale of the surviving human population and noted as a war hero. The festivities are soon interrupted by Cortana reporting "15 Covenant Capital Ships holding position just outside the kill zone", signaling the start to the Covenant Siege of Earth. UNSC Marine forces along with the Master Chief protect the station from the invading Covenant Naval infantry, and then head to the surface of Earth to New Mombasa to fight off the Covenant Army, led by the High Prophet of Regret. After the Covenant invasion force is halted by the UNSC defenses, the Prophet of Regret flees Earth with Keyes and her detachment in pursuit on In Amber Clad. The hasty in-atmosphere jump destroys most of the city of New Mombasa.

The story then turns back to the disgraced Sangheili Commander, who is given the chance of redemption by taking up the mantle of Arbiter, along with the imminent mortality of the task. The new Arbiter accepts and becomes the will of the Prophets, seeking to complete the impossible task assigned for redemption from his crimes. The Arbiter is tasked with the assassination of a Heretic Leader disillusioned with the Covenant following the events of Installation 04 up to its destruction. The Arbiter tracks the Heretic Leader throughout the gas mine where the Heretics sought refuge. When the Arbiter is finally able to face the Heretic Leader, 'Refumee asserts his belief that the Prophets have lied about the Great Journey, punctuating this with the entry of a Monitor. Before the Arbiter could learn more of the claims, the battle resumes, and the Heretic Leader is killed before any meaningful discourse taking place. Tartarus appears to extract him and Guilty Spark, preventing the Arbiter from learning any information from Spark. He leaves not knowing what caused the Heretics to betray their sacred oaths to the Covenant.

Turning back to the Master Chief's story, Keyes exits slipspace in her ship undetected with the Prophet of Regret unaware that he had been followed. To the surprise of the pursuers, they discover that Regret led them to another Halo Ring. Keyes soon determines that their objective is to Capture the Prophet of Regret and stop the Covenant from firing the Halo Rings, and the Chief is dropped onto the surface of Installation 05 with other UNSC personnel to do so. In the course of pursuing Regret, the Chief discovers with the aid of Cortana that the Prophet intends to personally activate Halo. Keyes decides that the new revelation about Regret's intentions warrants his death, which the Chief successfully achieves. But before being able to make his escape, the Covenant attempt to kill the Chief by glassing the area, and he jumps into the lake surrounding Regret's location. Incapacitated from the shock of the Covenant bombardment, the Chief is last seen being dragged into the depths of the lake by the tentacles of some creature.

The story now shifts back to the Arbiter on the Covenant Holy City in orbit around the ring. The Hierarchs had declared Regret's death to be the Elites' failure, and they were removed as the protectors of the the Prophets, who bestow the role to the Brutes, causing more tension between the Brutes and Elites who are already at odds with each other. Despite this the Arbiter is given a new mission to recover a Sacred Icon from the Library, having not died in his previous mission as all had expected. Making his way through the Quarantine Zone on the surface of Installation 05 seeking the Activation Index, the Arbiter makes his way into the Library and captures the Index along with Keyes and Johnson after they recovered it from its protective housing. Before he can take possession of the Index, Tartarus again intervenes in the Arbiter's task. After taking the Index into his own personal possession, Tartarus then reveals that the Hierarchs intended for his death to oust the Elites. His treachery revealed, Tartarus knocks the Arbiter unconscious down a shaft in the Index chamber to the abyss below.