The Heretic / Armory / Cairo Station
The opening cutscene shows the two major plot threads that will progress through Halo 2: the fate of Master Chief, Sergeant Johnson, and the rest of the human forces, which includes Captain Miranda Keyes, the daughter of the late Captain Jacob Keyes, and Lord Hood, apparently a ranking official in UNSC; and the fate of an unnamed gold Covenant Elite we come to know as The Arbiter, who was in command of the Covenant forces at Halo installation 04 and is consequently disgraced, accused of heresy, and then secretly sent on a special mission by the three Prophet Hierarchs of the Covenant: Truth, Mercy, and Regret.

The Arbiter is blamed for allowing the Pillar of Autumn to escape from Reach to Halo, as well as for the Master Chief's destruction of that ring. The Arbiter blames this on the Flood parasite and his inability to predict the Chief's actions. He is stripped of his rank and armor, and tortured by the white-mohawked Brute, Tartarus. These scenes also reintroduce us to the massive, hairy, apelike Brute race, first seen in the E3 2003 realtime demo. A more recent addition to the Covenant, they seem less sophisticated and less honorable than the Elites, although no less brutal and fearsome.

The Master Chief and Sergeant Johnson are decorated for their service on board the orbital defense station Cairo, but the ceremony is interrupted by a relatively small Covenant fleet led by the Prophet of Regret. The Cairo, as well as other orbital defense stations, such as the Malta, are boarded by Covenant forces. Lord Hood orders Captain Keyes to get aboard her ship, In Amber Clad and orders the Master Chief to repel the station's boarders.

While battling the Covenant boarders, Cortana reveals to you that the Covenant have placed a bomb on board, apparently planning to destroy the orbital stations and their deadly MAC guns to make it safe for the approach of a larger fleet. Master Chief locates this bomb, takes it with him to a hangar bay, and free falls through space with it, guiding it into a Covenant ship before safely hard-landing on the hull of In Amber Clad. In this level you'll encounter the first of several new units, the insect-like Drones that can fly.

Editor's Note: Longtime fans will, of course, recognize the final cutscene of this level from Halo 2's announcement trailer revealed in early 2002; the addition of the sea urchin-like Covenant bomb makes perfect sense, plot-wise, but detracts somewhat from the romance of the scene; in the original trailer half of the impact comes from wondering exactly what the Chief hopes to achieve by hurling himself out a hangar window, a question that conjures images of him improvising a one-man boarding party on a Covenant cruiser.

Outskirts / Metropolis
Johnson and the Chief head down to Mombassa, Africa in a Pelican and are shot down by a large four-legged Covenant land vehicle called a Scarab. They progress through the streets of Old Mombassa, across a suspension bridge into New Mombassa, and eventually find and destroy the Scarab. On the way you encounter the new-look Hunters with upgraded weaponry; they are no longer vulnerable to single shot kills. You'll also see Jackals without their tell-tale shields, which means they are toting Beam Rifles, the Covenant sniper weapon.

After the destruction of the Scarab, the cruiser belonging to the Prophet of Regret prepares to make a slipspace jump from just above the surface of the Earth. The Master Chief and Sergeant Johnson get aboard In Amber Clad just in time for the ship to propel itself into the slipspace wake of Regret's ship, following it. The ship's jump lays waste to New Mombassa.

Editor's Note: As many fans have already pointed out, Cortana notes in First Strike that she is able to use the slipspace engines and plasma weapons more accurately and efficiently than the Covenant themselves do, an indication of their continual misunderstandings of Forerunner legacies, whether technological or otherwise. That Regret's ship is able to execute this slipspace jump indicates that her knowledge has been assimilated by the Covenant, perhaps by the AI on the Ascendant Justice.

The Arbiter / The Oracle
The disgraced Elite is brought before two of the Hierarchs, Truth and Mercy (the third, Regret, appears as a hologram, as he does many times throughout the game) and told that he will not be executed outright, but will serve in a special position as The Arbiter; a role that is always suicidal and has been pivotal in many parts of Covenant history. To this end he receives new armor that will distinguish him from the rest of the Covenant.

The story here makes its first perspective switch, and players finally see that they are actually going to guide the actions of The Arbiter during gameplay. The first mission is to pursue an Elite called the Heretic, who the Hierarchs say is telling lies to the Covenant. He is hiding on a Forerunner station in the atmosphere of Threshold, the gas giant near the remains of Halo installation 04. The Heretic has supporters among various Covenant castes, including Elites and Grunts, which are distinguished from your own forces by differences in costume and coloration.

Throughout the level the Heretic taunts you with the statement that the Prophets are lying about the Great Journey. You pursue him throughout the station, including an interlude where he flees on a Banshee and you must give chase with the support of a Phantom and its three powerful plasma guns. Finally he ensconces himself behind a plasma shield as a powerful storm threatens to destroy the station.

In the second half we become aware of the fact that the Flood are loose on the station, and were possibly stored there or escaped there from Halo 04.

Editor's Note: Joe Staten on the LE DVD notes that this station apparently predates the Halo structures and was where Forerunners first "encountered" the Flood.

In an act of desperation, the Spec Ops Elite leader accompanying you gives his plasma sword to the Arbiter so you to cut the three cables that hold the station in place.

When you finally catch up with the Heretic in a hangar, he at first seems to try and persuade you to his cause, revealing that 343 Guilty Spark is with him, and again accusing the Hierarchs of lying without saying precisely what they have lied about. Then the Heretic fires on you and releases several holograms of himself. When you defeat him, Guilty Spark expresses regret because the Heretic's education had given him satisfaction. The Brute, Tartarus, arrives, takes 343 Guilty Spark prisoner, and the three of you leave the station before the storm destroys it.

Editor's Note: That the Heretic's efforts to convince you to believe him are half-hearted make the entire encounter seem a bit symbolic; as many players no doubt already suspect that he is, in fact, right about the Prophets, which is seemingly confirmed by 343 Guilty Spark, you may find yourself wishing that you had the option to instead join with him and turn on Tartarus; the kind of option offered players of games like Deus Ex. The fight against the Heretic and his holographic cronies is the first of Halo 2's three "boss battles" which feature enemies that must be fought with different tactics than other units.

Delta Halo / Regret
Switching back to the Master Chief, In Amber Clad exits slipspace behind Regret's cruiser to find they've arrived at another Halo installation. Sergeant Johnson is ordered to take his troops to the surface in Pelican dropships, while the Master Chief and a group of Helljumper ODSTs perform a hard-drop in pods. You link up with other marine forces and push your way through Covenant resistance, fighting among ancient-looking, vine-ridden ruins, eventually passing over a lake using two gondolas and under it through two underwater elevators, and arrive at a structure where the Prophet of Regret is delivering his sermon. Arriving at the structure, you look overhead to see an enormous Covenant fleet arrive from slipspace, including the massive Covenant capital, High Charity. After defeating the Prophet of Regret, the fleet turns its weapons on the installation, vaporizing it. You escape into the water and are captured by the tentacles of the giant plant-like character, Gravemind.

Editor's Note: Regret has been apologizing for his premature attack on Earth; I myself think it likely that he was targeted for elimination by the other Hierarchs anyway, and that even if the Master Chief had not killed Regret, Mercy and Truth would have ordered the fleet to vaporize him anyway. The fight with Regret is one of Halo's three "boss battles" in which you encounter enemies that must be fought in a particular way.

Sacred Icon / Quarantine Zone
On High Charity, the death of the Prophet of Regret at the hands of the Master Chief is used as justification for replacing the Honor Guard of Elites that protect the Prophets with Brutes. Both the Arbiter and the Spec Ops leader object to no avail, but the Elites are seriously disgruntled (no pun intended) and the first hints of the Covenant breaking apart along racial lines can be seen.

Tartarus drops the Arbiter off at a structure on Installation 05 called the Wall, a barrier guarding the Library. A protective shield prevents entry to the area; your first task is to deactivate this shield. The area is full of piston-like structures, some of which must be activated to gain access to other levels. The Wall is defended by Sentinels similar to those found on Halo 04, although some have more powerful beam weapons, and Enforcers, much larger foes that have shields and fire two weapons; one similar to the Needler and the other similar to the rocket launcher. In behavior and appearance they resemble the Juggernaughts (Nar) from the Marathon series.

When you finally arrive inside Halo 05's Library, you find that Sergeant Johnson and Miranda Keyes have arrived ahead of you. Tartarus seizes them and the Index and throws you off a precipice.


Gravemind
You awaken in the grip of Gravemind, who now has both the Arbiter and the Master Chief in his tentacles. Gravemind appears like nothing so much as the plant from outer space, Audrey II, in Little Shop of Horrors. He makes some cursory character judgments of the two, to which the Arbiter objects. There with Gravemind (or rather a part of him, depending) are the Prophet of Regret and 2401 Penitent Tangent, the Monitor of Installation 05. Regret and PT trade barbs, as Regret wants to finish his sermon. He claims that the Great Journey cannot take place until he does. PT disagrees, saying that Installation 05 has a service record that includes many simulated-- and one actual-- firing, and is ready to be operated. Regret accuses PT of having no knowledge of the Great Journey, and PT accuses Regret of ignoring basic protocols for the containment of the Flood. Gravemind interjects that the Great Journey and containment (the firing of the Halo) are the same, and teleports the Arbiter and the Master Chief to two places he thinks the Index might be in order to prevent the installation from being activated.

Editor's Note: Cortana's input is, remarkably, almost entirely missing from this exchange, as the only words she utters are "what is that?" Within the context of the game it is not made clear what the relationship is between the Flood infection, carrier and combat forms and Gravemind, if any. His name, as well as his absorption of Regret, seems to indicate that his nature is somehow related to preserving the mind and memories of dead individuals or perhaps even species, and in that sense, his ability to animate otherwise dead tissue might form some kind of connection to the Flood. Whether he directs the actions of individual Flood combat forms is unclear. That both the Chief and the Arbiter accept orders from their new companion is also quite strange, especially given that the Arbiter in particular seems suspicious of him.

The Master Chief is teleported into a room aboard High Charity where the prophets of Truth and Mercy are broadcasting the triumphant recovery of the Index and the impending Great Journey to the Covenant; with limited weapons, no way out of the room, and several waves of incoming Brutes and Grunts, the scenario is more than slightly reminiscent of the gravity lift room in the "Into the Belly of the Beast" chapter of Truth & Reconciliation in Halo 1. Throughout this level, Covenant discipline is breaking down; the Elites and Grunts are on one side, and Brutes, Jackals and Drones are on the other. However, this helps you very little, as all sides will attack the Chief if they get a chance.

Cortana asks to be dropped off into High Charity's systems, and for the rest of the game she assists you at various intervals, appearing on hologram generators throughout the city.

Pursuing the two Prophets with the Index throughout the city, when you arrive Truth and Tartarus has escaped on a Phantom with the Index, and Mercy has been attacked by a Flood infection form and left for dead, while Pelican dropships piloted by Flood begin raining down all over High Charity.

Editor's Note: The timing here is interesting, in that just at the moment where it is clear that the Chief has failed to secure the Index, Flood attack the city. It is possible that Gravemind is in control of Flood forces, and having deemed the MC's mission to be a failure, sees no reason to restrain his minions from attacking him. Or it could simply be coincidence.

Uprising
The Arbiter is teleported to the surface of Halo 05, in a forest environment similar to the Delta Halo / Regret level pair. Your task is, supposedly, to look for the Index, but this isn't mentioned in the objective texts at all, that instruct you to take revenge on the "Brute traitors"; a pejorative that seems unfair as the Brutes are following the Prophets' orders (however misguided) and it is, in fact, the Elites that are rebelling.

High Charity
In what is easily the most frustrating twist of the whole game, after arriving on the platform to find Mercy being sucked on by an infection form and hearing that Truth is headed "to Earth, to finish what we started" (presumably the Great Journey) In Amber Clad, apparently piloted by Flood, crashes into High Charity, and all over the city Pelicans carrying Flood start to appear.

Cortana orders you to head back through High Charity, now swarming with Flood as well as with Covenant civil war. Thankfully, the level is short. As it ends, Truth has arrived at the Forerunner spacecraft that forms the core and power source of the City, and is disengaging it to begin his journey to Earth. The Chief stows himself aboard, but Cortana stays behind on High Charity, saying that their failsafe plan-- the destruction of Halo 05 using the engines of In Amber Clad-- should not be executed remotely. Master Chief starts to promise to return for her once he has dealt with Truth, and Cortana urges him not to make promises he can't keep. The Master Chief then stows aboard the Forerunner craft.

Editor's Note: How Cortana intends to use In Amber Clad isn't entirely clear, as it had apparently crashed on the surface of High Charity, not Halo 05; perhaps they are close enough that the explosion would destroy Halo was well. In addition, that the center of the city is a Forerunner ship that powers it is not clear until the end; so at any moment before that they might have feared that High Charity would exit the area via slipspace, bringing In Amber Clad out of range of Halo 05 and making its destruction meaningless. Also, as she is not actually on board the ship, it seems that any detonation would, by definition, be "remote"; this has led some fans to speculate that she has another motive for remaining in the Covenant system, perhaps related to the "resistance" she vaguely mentions encountering during the level.

The Great Journey
As the Arbiter you arrive outside the Control Room structure of Halo 05 and greet the Spec Ops commander once again, this time at the controls of a Wraith tank. Tartarus and Captain Keyes are inside, and he intends to activate the ring. Using a combination of vehicles, including Wraiths and Banshees and (if you so choose, hijacked ghosts) you fight your way to a Scarab, which is then piloted by Sergeant Johnson, who rather inexplicably is open to helping you despite having apparently gotten no explanation of the current situation. He uses the Scarab to force an entry to the control room, where you land a Banshee and proceed inside to the final encounter with the Brute, Tartarus, which is Halo 2's third and final "boss battle" and the only one in which you get assistance from other units: in this case, Sergeant Johnson.

Tartarus is forcing Miranda Keyes to reunite the Index with the Core of Halo 05 to trigger the installation to fire. After you defeat Tartarus, she recovers the Index, and 343 Guilty Spark, brought there by Tartarus, explains that the interruption of installation 05's firing sequence has triggered a message to the remaining Halo installations, which will be put into a "standby" mode, in which they can be ordered to fire from a location referred to as The Ark.

Editor's Note: That Tartarus takes Keyes as well as the Index into the Control Room seems to indicate that the Covenant are now aware, if they perhaps were not earlier, of the essential role of humans, or Reclaimers, in the process of activating the Halo; something which is most likely offensive to them dogmatically, and perhaps the source of Regret's cryptic remark upon his death that "this time, none of you will be left behind."

Truth arrives at Earth aboard the Forerunner ship, and just as Lord Hood is about to order it fired upon (there is still fighting going on between human and Covenant forces on Earth at this time) the Master Chief signals him. Hood inquires about what the Chief is doing aboard the ship, and he replies "Sir.. finishing this fight."

After the credits, a final cutscene plays in which Gravemind addresses a holographic image of Cortana, and he says to her, "Now I will ask, and you will answer." She responds "shoot" to indicate her willingness to listen to his questions, and the scene fades out.

Editor's Note: This final bit of cutscene falls far short of the "betrayal" of humanity by Cortana that some have made it out to be; I take it more as an indication that even so far, what has been revealed to the human and Covenant sides regarding Halo is not the complete story, and that Gravemind himself may not have at his command all the facts.