The story of Halo 2 is told through in-game dialogue as well as cutscenes; the back-story to the game can be found in the game manual. Taking place shortly after the events of the novel Halo: First Strike, the game opens with the judgment and torture of a former Covenant Elite Commander, who is being punished by his fellow Covenant for failing to stop the destruction of the ringworld Halo by human forces during the events of Halo: Combat Evolved. It is revealed that the Covenant's interest in Halo lies in the religious belief that the activation of Halo would bring about the "Great Journey", which would allow them to follow the ancient Forerunners to the "divine beyond".[20] As the Elite Commander is tortured and branded with the mark of shame by the Brute Chieftain, Tartarus, a recognition ceremony is held for the humans Master Chief and Sergeant Major A.J. Johnson, who receive awards aboard Cairo Station, a MAC (Magnetic Accelerator Cannon) gun platform orbiting Earth, alongside Commander Miranda Keyes.[19]
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 MAC stations. These boarding parties are secretly carrying explosives designed to take out the MAC guns that protect Earth from attack.[21] After repelling the initial Covenant assault, the Master Chief locates and disarms the Covenant explosives 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.
Meanwhile, the disgraced Covenant commander has been given a chance to redeem himself as the "Blade of the Prophets", 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 him doubting his own beliefs about Halo.
Before reaching New Mombasa, Cortana decodes transmissions revealing that the flagship they are after carries the High Prophet of Regret, an important Covenant figure. The UNSC successfully repels the Covenant invasion force spread through the city, and the Covenant ship begins preparations for an emergency slipspace departure to an unknown destination. As Regret's ship disappears through the Slipspace portal, Keyes thrusts her ship after it, just before the portal closes and destroys the city with a massive shockwave. On the other side of the portal, they discover a second Halo installation dubbed "Delta Halo". Despite the Covenant's own ideas about the rings, Master Chief and the crew of the In Amber Clad know that the rings are actually weapons that if activated would wreak devastation on a galactic scale. Master Chief goes to the ring's surface to take down the Prophet of Regret while Keyes and Johnson attempt to secure the Index, an object the Covenant is after which can be used to activate Delta Halo. The Chief succeeds in killing Regret, but is then attacked by a Covenant fleet and eventually captured by a mysterious tentacled creature. [22]
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. The Prophets of Truth and Mercy send the Arbiter to retrieve the Index on Delta Halo. The Arbiter manages to obtain the Index before the humans do, but he is then betrayed by Tartarus, who reveals that the Prophets ordered him to kill the Arbiter. He takes the Index and shoots the Arbiter down into a hole in Delta Halo's library. [23] The Master Chief and the Arbiter meet upon the release of the Flood, a race of parasitic creatures, from Delta Halo. A mysterious and intelligent Flood creature called the Gravemind has captured them both and teleports the Arbiter and Master Chief to separate locations in an attempt to prevent The High Prophets from activating Delta Halo.[24] The Arbiter is sent to an area on Delta Halo, just outside the ring's activation center. There, the Arbiter discovers that the Brutes have massacred many of the Elites and most of the ruling Elite Councilors, betraying the Elites by the order of the Prophets. Having finally realized the truth about Halo and the Covenant, the Arbiter rallies his surviving fellow Elites and leads an uprising against the Brutes. Master Chief finds himself aboard the Covenant Holy City High Charity, a gargantuan mobile space station that serves as the Covenant capital city, and pursues the remaining Prophets. During his mission, he finds himself in the middle of the 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 Prophet of Mercy is killed by the Flood, leaving only one remaining Prophet, Truth, who 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 in case Tartarus activates the ring.[25] Tartarus does indeed activate the ring, but the Arbiter with the help of fellow Elites, Sgt. 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 dangerous "standby" mode so they can be remotely activated from the Ark.[26] Meanwhile, the Forerunner ship that Master Chief has stowed away on approaches Earth. The remaining orbital forces are in the middle of another battle with Covenant ships. On Cairo Station, Lord Hood contacts the Chief 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.