Halo 2
Halo 2 continues the story of the UNSC's war for survival against the Covenant. The story picks up with Spartan 117 having just returned to Earth a hero. The time in between the first game and Halo 2 is documented in the novel "Halo: First Strike" by Eric Nylund.
At the same time the Spartan 117 is recieving a medal for his actions in Halo: CE the Covenant Shipmaster; an elite if high rank who was in charge of the forces at Installation 4, is being tried by the Covenant Council for Heracy. Eventually the shipmaster is found guity, stripped of his reank, publicly tortured, branded with a mark identifying him as a heratic and sentanced to death.
It is at this point that a small Covenant force, led by the Prophet of Regret stumbles upon Earth. They are searching for Forerunner technology as usual and the Prophet of Regret believes something very important is on Earth. Rather than engaging the superior Earth forces the Covenant engage the UNSC defense platforms by attacking Earths defense platforms by boarding them and setting off large bombs. Spartan 117 successfully defends the defense platform Cairo and returns the Covenant to one of their larger ships, destroying it in the process. Spartan 117 then joins the ship In Amber Clad on an attack of the Prophet of Regret's ship. The Prophet, fearing capture, engages a slipspace transit while still in Earth atmosphere, destrying the city of New Mombasa in the process. The In Amber Clad follows Regret through the slipspace rupture and both ships arrive at Installation 5.
The Prophet of Truth, as head of the council, commutes the heretic shipmaster's death sentance into service as "The Arbiter." The Arbiter is a holy position held by many elites throughout the millenia that the Covenant has existed. He is the silent assassin of the Council, sent on the most dangerous suicide missions. The Arbiter's are revered as heroes of the Covenant. They also die, without exception, in this service.
The Arbiter is sent on several dangerous missions which culminate in the capture of Installation 4's wayward Monitor, 343 Guilty Spark. Eventually the Arbiter is betrayed by the council, specifically through the actions of the Brute commander Tartarus assaulting him, taking custody of Guilty Spark 343 before he can reveal the true purpose of the Halo Array and leaving the Arbiter for dead on Installation 5.
Spartan 117 hunts and eventually kills the Prophet of Regret on Installation 5. This leads the council to conclude that the elites are no longer capable of protecting the Prophets and a civil war within the Covenant between the Elites and the newly appointed protectors of the Prophets, the Brutes begins. After Spartan 117 kills Regret a bombardment from space leaves him near death on Installation 5.
The Flood has been loose for some time on Installation 5. Because of their religious zealotry the Covenant is once again seeking to fire the Halo Array. This will of course kill all sentient life in the Galaxy. The Flood super consciousness called "Gravemind" collects the Arbiter and Spartan 117. It knows that Spartan 117 is already aware of the purpose of the Halo Array but the Arbiter is still blinded by his devotion to the Covenant. The Gravemind sends the two on separate missions to stop the firing of the Halo Array. In the process the betrayal of the council, the war with the Brutes and the true purpose of the Array is revealed to the Arbiter. Joining with the last of the UNSC forces the Arbiter and his fellow elites attempt to stop the firing of the array. In a climactic battle with the Brute Chieftan Tartarus, Amanda Keyes, captain of the In Amber Clad and the daughter of the Captain of "The Pillar of Autumn" removes the index and stops the firing sequence of the Halo Array. The Brute Chieftan is killed in the battle.
Meanwhile Spartan 117 is attempting to stop the fleeing Prophets of Truth and Mercy from heading to Earth where a new installation referred to as "The Ark" may be. Once the firing sequence is stopped the Gravemind turns on everyone and attempts to kill and consume every living creature on the installation. During the battle the Flood assaults and establishes a foothold on the Covenant Mobile P{lanatoid Station, "High Charity", a station so large it contains a small star inside it yet can still move through slipspace with the power of the Forerunner ship that serves as it's energy source. The Flood kills the Prophet of Mercy but Truth escapes both the Flood and Spartan 117 to the waiting Forerunner ship inside High Charity, decouples the ship from High Charity and heads for Earth and the Ark. Just as the forerunner ship ship is launching Spartan 117 leaves the AI Cortana behind in High Charty's computer system with instructions to overload the now Flood inhabited In Amber Clad's reactors and destry High Charity and makes it onto the departing Forerunner ship just as it departs.
In the closing scene of the game Spartan 117 returns to Earth aboard the Foreruner ship and contacts UNSC command, informing them of Truth's intent. A cut scene after the credits roll reveals that the AI Cortana was unable to destroy High Charity and is captured and interrogated by the Gravemind.