This post was created in response to grey's request for storyline information. For those who haven't played Halo 2 and want to know how the story proceeds, here's the lowdown. Note that this is all from my own recollection of the game and the cutscenes available at http://halo.bungie.org/.
Halo 2
The story of Halo 2 begins with a cutscene as a Covenant Elite is interrogated by three Prophets, and is blasted over his inability to safeguard Halo and kill the human responsible for its destruction. His demand to "continue his campaign against the humans" is rejected and told that he will be left behind when the Great Journey begins. He is then hauled away by several Brutes.
The Master Chief is introduced on an orbiting defense station above Earth, retrieving gear and performing the typical control initialization sequence. Chief meets up with Sgt. Johnson (his return is detailed in "First Strike") and boards a tram to transit to a ceremony, where both he and Miranda Keyes – the late Captain Keyes' daughter - are presented with awards.
The perspective then switches to that of the Elite, who is forcibly stripped of his armor and branded with the Mark of Shame, identifying him as a Heretic (a Covenant member that has either failed the Prophets or disagrees with their teachings.) This is the first clue that all is not well within the rank and file of the Covenant. As the cutscene ends, the viewpoint switches back to Master Chief and the action begins.
As in Halo, Master Chief must go throughout the ship, forcing the Covenant boarders away from sensitive areas. Tension mounts as the Covenant leave other defense platforms, only to have them explode. It's evident that the enemies have planted bombs, and the Chief is given the task of disarming the one on Cairo Station.
Of course, merely disarming the bomb isn't much to Chief's style. In a grand spectacle of showing off, he releases the airlock on the station, free-falling from the defense platform holding onto the Covenant artillery. As he passes through the middle of a Covenant ship, he reactivates the bomb and pushes off, destroying the Covenant carrier and landing back on top of the human spacecraft (In Amber Clad) below.
Continuing the similarity between Combat Evolved and Halo 2, the ship crash-lands on Earth in Old Mombasa. Master Chief, the Sergeant and the Marines defend themselves from various waves of Covenant in a city courtyard, then proceed to traverse through the old city, doing what Marines do best: take names and kick ass. There are a few good scenes here, but eventually Chief gets to proceed to "New Mombasa" and take out the Scarab, the giant mechanical robot that's been terrorizing the city. The orbiting Covenant cruiser (with the Prophet of Regret on it) tries to escape, but Miranda and In Amber Clad follow the behemoth into Slipspace.
Fade to black. The outcast Elite is shown being dragged along by three Brutes – two lesser and one more important one, Tartarus. He is brought before the Prophets Truth and Mercy and given a special purpose: to become the Arbiter, one of a long line of Covenant followers who seek out heresy within the ranks, and eliminate it. The position is suicidal – in fact, the Prophets mention that once his mission is complete, he will die like all the others before him. The Elite accepts his new armor and asks what they would have him do.
The Arbiter is taken to a platform above an incredibly large planet – a gas giant. As the cutscene fades to white, the first plot spoiler of the game is revealed: Control is given back to the player to become the Arbiter. This development helps both the Covenant and human storyline be told in a more specific way, but is an incredible development for the Halo series. The Arbiter's task is to seek out and destroy a Heretic preaching against the Prophets and their Great Journey.
As the Covenant forces along with the Arbiter enter the Gas Giant laboratory, one of the Elites pauses and sniffs the air. "That stench – I've smelled it before," he notes as the music ramps up. Of course, the goal here is obvious: the reintroduction of the Flood. Now, the Arbiter must battle them in order to reach the Heretic. Of course, the Heretic is trying to escape the Arbiter and the crew of Covenant set on silencing him, and flies away in a Banshee. The Arbiter follows him to another platform and eventually confronts the Heretic.
The Heretic is asked "Who has taught you these lies?" A familiar humming re-emerges: the Monitor, 343 Guilty Spark, flies into the scene, ready to stir up his usual brand of trouble. The Arbiter calls him "the Oracle", but before any serious discussion can be had, the Heretic calls up two hologram units and forces the Arbiter to kill him. As the Oracle and the Arbiter are almost ready to work out what's really happening, Tartarus "grabs" Guilty Spark with an energy hammer and tosses him into the gravity lift. The Arbiter is shocked at the crude disrespect shown to the Oracle, but follows Tartarus to leave the system.
In Amber Clad, after flying through slipspace, the ship approaches another Halo construct, titled Delta Halo. Miranda orders the Master Chief and the Marines to drop onto the surface and get their bearings. Traversing through old Forerunner structures and battling the usual assortment of Covenant, Chief eventually finds a hologram of the Prophet of Regret. Cortana translates the meaning of the incantations: he's planning to activate the Halo construct ahead of schedule, so Master Chief must find him before that happens.
Eventually (and after traveling over several gondolas, large platforms intended for over-water transition,) Chief arrives at the temple where Regret has holed himself up. There's no question about it – the Prophet finally gets what's coming to him as Chief kills the hierarch. Unfortunately, if the Covenant didn't have a reason to retaliate before, now the Chief is under severe attack. As the structure is destroyed, he falls into the large body of water under the gondolas and platform. Sinking down, a voice booms out: "This is not your grave...but you are welcome in it." A pair of tentacles grabs the Chief, pulling him down to the depths of the water.
Meanwhile, all is definitely not well with the Covenant. The Elites have been removed from their positions as honour guards of the Prophets, and replaced with the Brutes. The Elites are not at all happy with this change, and the "Great Journey" is starting to sound less and less appealing. The main commander of the Elites nods to the Arbiter when they pass by – a subtle signal of change in alliance for the respective races within the Covenant. The Arbiter is given an additional mission: to retrieve the Index for the Prophets.
Nearly achieving his goal, the Arbiter is ready to retrieve the Index – only Miranda and Sgt. Johnson have beaten him there. Tartarus decides to make an appearance again: capturing the humans and betraying the Arbiter as he tries to retrieve the Index. Tartarus then takes off to deliver the Sacred Icon. As the Arbiter falls, another pair of tentacles snatches him.
The Master Chief and the Arbiter are now united by an enormous Flood-like creature named Gravemind, who refers to himself as "the manifestation of all your sins." Gravemind is well aware of the Prophets' mission and splits the Arbiter and Chief up, sending them to look for places that the Index would likely be. The Master Chief is directed to High Charity, while the Arbiter is sent to the Control Room on Delta Halo.
On High Charity, a sort of civil war is erupting – parts of the Covenant have seen through the Prophets' suicidal Great Journey and now the Elites, Grunts and Hunters (all Heretics, now) are fighting against the Brutes, Jackals and Drones (who are sticking by the Prophets and their vision.) Master Chief nearly gets to the Prophets in time to halt them, but is too late once again. The human ship, In Amber Clad, crashes into High Charity – and Gravemind has tagged along, using the human forces.
The Prophet of Truth starts heading for a Forerunner ship to lead the remaining Covenant to Earth, but Mercy is left behind and consumed by the Flood. Sgt. Johnson and Miranda are taken on separate Phantoms with Brute guards to Delta Halo's Control Room, with Tartarus accompanying them. The Master Chief starts making his way towards the Forerunner ship, leaving Cortana behind to supposedly activate In Amber Clad's fusion reactors (much like the Pillar of Autumn did to destroy Halo in the first game) if the ring starts to fire its primary weapon.
The Arbiter and the lead commander of the Elites, all the while, are trying to make their way to the Control Room. In order to blast their way in, they opt to take a Scarab, but Sgt. Johnson's arrived there first – seems there was a nasty little accident with his Phantom. The Arbiter, while still very much an Elite with hatred for humankind, agrees to help the Sergeant and the Marines to stop Halo from firing.
As the Arbiter arrives, Tartarus has just forced Miranda Keyes to act as the Reclaimer, pushing the Index into Halo's control panel and initiating the firing sequence for the ring. The Arbiter has had enough of the Brute and with some help from Sgt. Johnson, manages to kill Tartarus { in a poorly-done boss battle, ugh. } Miranda grabs the Index and prevents Delta Halo from firing, but protocol for the Halos indicates that they're all now on standby mode, waiting for a command from the primary control – the Ark. Where might this Ark be, then?
Master Chief has grabbed hold of the Forerunner ship and is hurtling towards Earth. He instructs the UNSC not to fire on the vessel – and when asked what he's doing there, he replies: "Finishing this fight." Fade to black, roll credits. Game's over.
After the credits, the scene switches to Gravemind interrogating Cortana on High Charity. Gravemind notes that "now I will ask, and you will answer"; Cortana replies "Shoot."


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