Thel 'Vadamee tracks the Heretic Leader throughout the gas mine (battling the Heretics and the Flood) where the Heretics sought refuge. Thel 'Vadamee is tasked with the assassination of a Heretic Leader, who is disillusioned with the Covenant following the events of Installation 04 up to its destruction. The new Arbiter accepts and becomes the will of the Prophets, seeking to complete the impossible task assigned for redemption from his crimes. The story then turns back to the disgraced Sangheili Commander, Thel 'Vadamee, who is given the chance of redemption by the High Prophets of Truth and Mercy in taking up the mantle of Arbiter, along with the imminent mortality of the task. The hasty in-atmosphere jump devastates the city of New Mombasa destroying the Space elevator and scattering its wreckage for miles around. After the Covenant invasion force is halted by the UNSC defenses, the Prophet of Regret flees Earth with Miranda Keyes, Captain Keyes' daughter, and her detachment in pursuit on the UNSC In Amber Clad. After sending the bomb that the Covenant had placed on the station back into space (destroying several ships) he landed on the UNSC In Amber Clad and then they head to the surface of Earth to New Mombasa to fight off the Covenant Army, led by the High Prophet of Regret. UNSC Marine forces along with John-117 protect the station from the invading Covenant Naval infantry but other stations were destroyed by the Covenant. 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.

Avery Johnson, recently promoted to Sergeant Major, arrives to take John-117 to an awards ceremony overseen by Fleet Admiral Terrence Hood for the dual purposes of awarding meritorious acts and boosting the morale of the surviving human population and noted as a war hero (John-117 has already received all medals except for the 'Prisoner of War' medal).

The story then turns to Earth's Orbital Defense Platform Cairo Station, where Master Chief Petty Officer John-117 receives the new MJOLNIR Mark VI armor from the Master Gunnery Sergeant. 'Vadamee is then stripped of his rank and branded with the Mark of Shame by Tartarus, the Chieftain of the Jiralhanae. Despite his insistence that the Flood hampered his abilities, the Hierarchs who lead the council, the High Prophets of Truth, Mercy, and Regret, deem him guilty of failing to protect the Sacred Ring. The former Supreme Commander of the Fleet of Particular Justice, Commander Thel 'Vadamee, is being tried before the High Council for his failure to protect Halo. The game begins on High Charity, the mobile capital city of the Covenant. 3.1.1 United Nations Space Command Standard.

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