the game opens with the judgment and torture of the former Covenant Elite Supreme Commander of the Fleet of Particular Justice, who is being punished for his incompetence of safeguarding Installation 04. This is juxtaposed with the recognition ceremony of the Master Chief and Sergeant Avery Johnson receiving awards aboard Cairo Station, a MAC gun platform orbiting Earth, alongside Miranda Keyes. It is revealed that the Covenant' s interest in Halo lies in the belief that the activation of Halo would bring about the " Great Journey" , which would cleanse the universe of lesser lifeforms (including the Flood) and allow them to follow the Forerunners to their mysterious destination, where they would exist as gods.

Soon after the commencement of Master Chief' s ceremony, a Covenant fleet jumps out of slipspace near Earth. The Covenant proceeds to send boarding parties towards a battle cluster of stations. These boarding parties are secretly carrying explosives designed to take out the MAC (Magnetic Accelerator Cannon) guns that protect Earth from attack. Master Chief finds and disarms a bomb located on Cairo Station with the help of Cortana, while the flagship of the Covenant fleet speeds past Earth' s defenses and heads toward Earth itself. Master Chief and Cortana join the UNSC ship In Amber Clad, which is en route to New Mombasa to deal with the Covenant flagship.

Before reaching New Mombasa, Cortana decodes transmissions revealing that the flagship carries the High Prophet of Regret. The UNSC successfully repels the Covenant invasion force with the help of Master Chief, and the Covenant ship begins preparations for a slipspace jump to an unknown destination. The ship makes the jump, and the city is destroyed in the shockwave. To avoid destruction, In Amber Clad follows and discovers a second Halo installation dubbed " Delta Halo" . The crew of In Amber Clad learns more about the Covenant' s belief regarding the Halos, and Master Chief ultimately slays the High Prophet of Regret while Keyes attempts to secure the Index to prevent the activation of Delta Halo.

The action switches to the condemned Covenant fleet commander assuming the role of the Arbiter. His first mission is to silence a heretic who doubts the Prophets' teachings, in turn starting the Arbiter along a path which ultimately results in Arbiter doubting his own beliefs. Seeds of discord are further sown within the Covenant when the Prophets decide to grant the Brutes the job of protecting the Prophets instead of the traditionally favored Elites. During his missions, The Arbiter realizes the danger that the rings represent: they are weapons designed " to destroy all sentient life in the galaxy" according to the Oracle, not the religious artifacts the Covenant believes them to be.

The Master Chief and the Arbiter meet upon the release of the Flood from Delta Halo. A mysterious Flood creature called the Gravemind sends the Arbiter and Master Chief in separate directions to prevent The High Prophets from activating Delta Halo. Master Chief finds himself aboard the Covenant Holy City High Charity, a gargantuan space station, and pursues the remaining Prophets. During his mission, he repeatedly sips from a flask of delicious Irish whiskey, and finds himself in the middle of an erupting Covenant civil war between the Brutes and the Elites. After capturing In Amber Clad, the Flood, led by Gravemind, arrive at the city and begin to consume and infect the populace. The only remaining High Prophet, Truth, escapes on a Forerunner vessel hidden in the core of High Charity. The Master Chief stows away on board while Cortana stays behind in order to detonate the In Amber Clad' s engine reactors to destroy Delta Halo and High Charity if Tartarus activates the ring. The Arbiter, with the help of fellow Elites and Avery Johnson and Keyes, manage to stop the firing. However, the unexpected shutdown causes the ring to send a signal out to the other remaining Halos, sending them all into a " standby" mode so they can be remotely activated from the Ark. Meanwhile, the Forerunner ship that Master Chief has stowed away on approaches Earth. One of Earth' s remaining orbital forces contacts him and asks what he is doing aboard the Forerunner ship. He replies, " Sir, finishing this fight," ending the game with an abrupt cliffhanger and setting the tone for Halo 3.

During his mission, he repeatedly sips from a flask of delicious Irish whiskey,