Intro to Halo 2

The game begins shortly after the events of Halo: Combat Evolved. Before the game begins, we catch a small glimpse of the Covenant via a cutscene. For the first time, we learn a little bit about the society of the Covenant. An Elite holding the rank of Supreme Commander is brought before the High Council, to be evaluated for his "colossal failure". He is wrongfully accused of heresy, and branded by the Brute Chieftain Tarturus with the Mark of Shame. It is revealed that the Elite is the former Supreme Commander of the Fleet of Particular Justice, the Covenant fleet that destroyed Reach, as well as the one which failed to safeguard Alpha Halo.

John-117 (Master Chief) begins on Cairo Station, one of the three hundred Orbital Defense Platforms on station at Earth. There, his armor is upgraded to Mark VI, and he is taken to a ceremony, celebrating the 'victory' at Halo. As this takes place, the Prophet of Regret arrives in-system with a small Covenant Armada. The Covenant send out waves of boarding parties to destroy the extremely powerful Orbital Defense Platforms with bombs. The boarders succeed on two stations, the Malta and the Athens, but the Master Chief, with the help of Cortana, disables the bomb on the Cairo; following this, as Regret's forces are attempting to land on Earth, John takes the bomb, and, using an airlock, freefalls through space, passing through part of a Covenant Carrier, where he reactivates the bomb, before being picked up by the UNSC frigate, In Amber Clad.

The battle is then taken to the surface of Earth, to New Mombasa, where Master Chief and the Marines attempt to push back the invading forces. Originally, John's mission was to attempt to board Regret's Carrier and capture the Prophet of Regret, but once the Scarab that was leading the Covenant attack was destroyed, his ship attempted to escape. This led to In Amber Clad, with Sergeant Johnson, Miranda Keyes and John 117 aboard, following the ship, as it made a Slipspace jump inside the city.

[edit] The Arbiter

The Arbiter.The Elite branded in the opening cutscene was sentenced to be executed; however, rather than have him slain outright, the Prophet of Truth and Mercy made the decision to give him a chance to regain his lost honor and serve the Covenant again.

The Prophet's offered him the role of Arbiter, the highest honor for an Elite during a time of instability. As Arbiter, he must conduct missions for the prophets that are almost impossible and almost certainly suicidal in which the current Arbiter will die as a martyr for his race. This is part of the Great Journey, which is a religious series of events that the Covenant heavily believes in. In order to complete their "Great Journey", the Covenant must activate a Halo installation. It is assumed that the "Great Journey" is referring to a space age rapture that will kill all life in the galaxy, and there will be a "Judgment Day" where all will be judged and the ones without sin will join the gods of the Covenant.

As his first mission as Arbiter, the Elite must eradicate a group of Heretics who have separated themselves from Covenant society. They reside in a gas facility near the destroyed Alpha Halo. The Arbiter was to die during this mission, but he escaped death and defeated the Heretic leader. This is the first time we witness conflict within the Covenant society as the heretics constantly tell the Arbiter he is a fool for believing in their Great Journey and the lie of the Prophets.

[edit] Discovery of Installation 05

Master Chief battles Regret.During this time, Master Chief, aboard the UNSC ship In Amber Clad, is transported to the vicinity of another Halo ring - the Delta Halo - perhaps many tens of thousands of light years from Earth, on which they land. This time, Cortana and Master Chief are well aware of the dangers in Halo. They quickly begin to search for a way to disable it before the Covenant are able to reach it. Master Chief discovers the location of the Prophet of Regret, and must infiltrate his temple and kill him before he can activate the ring. Rather than aiding his fellow hierarch, the Prophet of Truth calls back the Phantoms that would have provided Regret with help and instead destroys the temple with an Energy Projector. Narrowly escaping the destroyed building, Master Chief is then captured by Gravemind.

[edit] The Index and Gravemind
The Arbiter remains alive and is sent by the Prophets to Delta Halo. The Arbiter is sent to lower the contamination shields surrounding the Library so the Covenant ships may approach. It is revealed to the Covenant that the Flood have been released, however, the Covenant still press forward. Before he can complete his mission, Sergeant Johnson and Commander Keyes seize the Index, forcing the Arbiter to combat them. This results in Keyes and Johnson being unconscious. After retrieving the Index, Brute Chieftain Tartarus takes it from The Arbiter. The Arbiter objects, saying the Prophets will not stand for his actions, to which Tartarus laughs, informing him that the Prophets sent him to kill the Arbiter. Tartarus then throws the Arbiter into the seemingly bottomless core of the Library and takes Keyes and Johnson captive, presumably to activate the ring.

In the next cutscene, the Arbiter is caught in a green vine-looking object. He is next to Master Chief who has just regained consciousness. A giant being known as Gravemind, a form of the Flood, holds the two. He comments on the differences between Humans and Elites and informs the Arbiter of the Prophets replacing Elites with Brutes as they don't feel Elites can protect them any longer. He tells of their killings and then reveals that he has reanimated the corpse of the Prophet of Regret as part of himself. He also has with him 2401 Penitent Tangent, the monitor for Delta Halo. 2401 and Regret argue about the truth behind The Great Journey, Regret saying it will bring salvation while 2401 disagrees with the Covenant's responsibility in handling Halo and the Flood. Gravemind comments that the Covenant will not find the salvation they are looking for. He then transports both Master Chief and The Arbiter to places where they will likely find the Prophet of Truth who has the Index, which Gravemind wants back. It is now that the Arbiter realizes the Elites have been betrayed, but still finds it hard to believe.

[edit] High Charity
John-117 is transported to High Charity where he inputs Cortana into the Covenant network, separating himself from her. She discovers that the Covenant are in the middle of a civil war with the Prophets, who are executing a genocide against Elites, feeling the Elites can not protect the Prophets. Brutes are put in their place and are sent to wipe out the remaining Elites. As Master Chief travels through the ancient planetoid, he encounters much conflict between Covenant, allowing for less resistance against himself, making it easier for him and Cortana to infiltrate the area. Their success leads the Prophets to promote this as a failing of the Elites rather than acknowledging their forces are scattered and unorganized.

When Master Chief reaches the other prophets (Truth and Mercy), he sees Sergeant Johnson and Miranda Keyes get captured and the Flood starts to attack. In the attack the Prophet of Mercy dies. After Master Chief gets close to the Forerunner ship, he tries to grab Cortana but can't because she does not want to risk a remote detonation of In Amber Clad so she stays on and becomes separated from the Master Chief and is left within a computer on High Charity.

[edit] The Great Journey
The Arbiter is transported to a forest and finally realizes the truth in Gravemind's words after being attacked by a group of Brutes, who were once his allies. He rallies Elites and makes his way to the entrance of the structure. Once making his way through the cavern, he reunites with Rtas 'Vadumee, an Elite Commander. They combine forces with Sergeant Johnson and help get the Scarab to the middle structure to make an entrance for the Arbiter to get to Tartarus. He then makes his way to the center of the structure to stop Tartarus from activating the ring.

The Halos, we learn from 343 Guilty Spark, were built to prevent the Flood from spreading throughout the Galaxy, and that the Forerunners who built it were wiped out when they fired it as a "weapon of last resort" at some point in the remote past. In spite of this, the Brute leader Tartarus forces Miranda to activate the ring in preparation to fire, to bring about - in his eyes - the Great Journey. The player must fight Tartarus (and on higher levels other Brutes) to retrieve the Index and stop the activation of Installation 05.

The Index is retrieved and the Installation cannot fire. 343 Guilty Spark reveals that although the Index was removed before Delta Halo had time to complete its firing sequence, it sent signals to other Installations in the Galaxy, putting them on standby mode. Now, they can only be activated remotely from the Ark.

After that scene the camera moves to a picture of Master Chief apparently aboard the Forerunner ship. When asked by Lord Hood why he is on the ship all he says is, "Sir, finishing this fight."

After the credits roll, a teaser for Halo 3 shows where the Flood has completely taken over High Charity with the Gravemind saying "Silence fills the empty grave now that I am gone, but my mind is not at rest, for questions linger on." The scene then changes to a stand in the council chambers of the Hierarchs the Gravemind then says "Now I shall ask, and you shall answer." It then changes to Cortana saying "Alright, shoot".

There is no novelization of this game yet. It is possible that a novelization that follows the canon laid down by the previous three novels might differ somewhat plot wise from the game, due to various differences between the game and the other novels.