At the Covenant city High Charity, a lone Elite commander stands before a Council to explain the loss of the Halo ring to his superiors. The Elite mentions that only one human ship, the Pillar of Autumn, escaped Reach and managed to land on Halo. The Council blames the Elite for letting the humans land on Halo and accuse him of heresy. The three Prophets of the Covenant decide to brand the mark of heretic on the Elite and have him imprisoned. As the Brutes escort the Elite, they come upon a device standing infront of several huge stands of onlookers, and he is cuffed and tortured. As it seems the worst is over, the Brutes remove the Elite's armor and a torch-looking device comes out of the ground; the tip is glowing red. A Brute snatches it and presses it against the Elite's flesh. He screams out in pain and agony...

As the Chief leaves the bridge and arms himself, he moves quickly with several Marines to meet a boarding party of Covenant. They enter the area and position themselves. The window shows a Covenant boarding ship latched onto the Cairo and the locked doors begin to weld open, signaling that the Covenant are here. The door bursts open and several Elites and Grunts rush in. They are greeted by the machine gun fire of the Marines. As the final Grunt is killed, the Chief runs by the charred remains of the blown door and begins to fend off each Covenant invader in the station. In time, two of the neigboring firing stations, the Athens and Multsur, are blown up and Cortana figures that a bomb was brought along, and there's likely one in the Cairo, too. The Chief then sets off to find the Covenant bomb. He fights his way through several areas of the Cairo and finally reaches the room with the bomb. He kills the Elite's guarding it and lets Cortana defuse it. The Chief then gets on the radio and asks permission from the admiral to "give the Covenant back their bomb." The admiral grants him permission and the Chief begins to drag the bomb out into the elevator. They reach the airlock bay and open it. The vaccum of space begins to pull the bomb slowly, and suddenly it is picked up and thrown out. The Chief grabs onto it and floats into outer space with it. Infront of him, the battle rages on as the human fleet tries to pursue to retreating Covenant. A Halcyon-class battleship shoots by infront of him, only to be destroyed by the cannon of a Covenant capital ship. Two longsword fighters fly by, approaching the Covenant ship and desperse it's load of bombs onto it. A hole is blown into the armor and the Chief floats in with the bomb. The ship's reactor is there, and the Chief reactivates the bomb and pushes it with his legs before thrusting himself away. As he leaves, the bomb destroys the Covenant ship and the Chief lands right into Commander Miranda Keyes's ship In Amber Clad. They then head to Earth to sweep up the remaining Covenant ship on Earth...

On Earth, the Covenant ship stationed above a city contains the Prophet of Regret. The humans make it top priority to secure the Prophet and find out why he came to Earth, to this location. En route to the objective via pelicans, a Covenant scarab comes up and shoots down each Pelican effortlessly. The Master Chief and the crew of the shotdown pelican make their way through the city towards the gravity lift of the Covenant ship. As they near, the scarab shows up again and the Chief is forced to destroy it. As it is destroyed, the Covenant ship prepares to leave the city by jumping into slipspace inside the city. In Amber Clad receives permission to intercept the ship before it leaves but is too late as they too jump into the same slipspace rupture as the Covenant ship. The city is destroyed by the slipspace aftershock...

The Elite is being dragged through the cellblocks of the detention center by three Brutes when they come upon the Mausoleum of the Arbiter. Inside are the Prophets of Truth and Mercy. The Propets begin to tell the Elite of the Arbiters, each one created in a time of crisis to deal with drastic situations. They offer the Elite the opportunity to become the Arbiter, and he accepts. Three Phantoms leave High Charity inbound towards a Forerunner facility hovering above a storm-ridden planet where a rebel band of Covenant reside. The mission is to silence a heretic leader and all who follow him. The squad lands and begins to work their way into the facility. After searching the facility and narrowing down the position of the heretic leader, they find the Flood have been released and are running rampant throughout the area. As they get to the area where the leader is, he boxes himself in and the only way to chase him out is to cut loose the structure they're in from the main structure. The Arbiter cuts the station loose and begins the chase for the heretic leader. He catches up with him and the heretic leader tells the Arbiter that the Prophets are lying about the Halo rings. To prove himself, 343 Guilty Spark (or Oracle, in Covenant vocab) comes but before he can explain everything, the heretic leader tries to kill the Arbiter. The Arbiter kills him and Tarturus, Chieftain of the Brutes, captures 343 Guilty Spark and they head back to High Charity...

The Covenant ship exits slipspace and In Amber Clad follows right behind it. The ship is dead in space until the crew can return it to operational status. Coming into view is another Halo ring. Commander Keyes has Master Chief take a squad of Orbital Drop Shock Troops (ODST's) down to the new Halo ring and continue the hunt for the Prophet of Regret. The Chief and the ODST's land on Halo and begin to make way towards the temples they find near the landing zone. In the process, Cortana finds out that the Prophet of Regret wants to activate Halo. Commander Keyes decides to get the Index, which activates the Halo ring, before the Covenant does. She has Chief kill the Prophet first before joining them. After taking gondolas from temple to temple, they reach the main temple and find the entire Covenant fleet accompanied by the city High Charity exit slipspace above Halo. The Chief continues into the temple and fights and kills the Prophet of Regret. As he is leaving, a Covenant ship begins to destroy the temple. The Chief jumps off the platform and into the lake before it is destroyed, but is knocked unconscious. Suddenly, tentacles appear and capture the Chief. A distant voice echoes, "This is not your grave, but you are welcome in it..."

The Arbiter walks into the Sanctum of the Heirarchs, seeing that the Honor Guard of Elites are having their armor and weapons taken from them by the Brutes. As the Honor Guard is being replaced, the Arbiter walks into the room where the remaining two Prophets are speaking to a Elite commander. The Prophet of Truth mentions that the death of the Prophet of Regret has made it clear that the Elites can no longer guarantee their safety. As the Elite commander leaves to inform the Council, Truth tells the Arbiter that the information they extracted from 343 Guilty Spark tells them that they must retrieve a Sacred Icon (the Index) from the Library before they can activate Halo, believing it will bring them salvation for all. They give the Arbiter the mission and he sets out to the Library, where the Flood and Covenant are battling. As the Arbiter fights his way through the area and lowers the shields protecting the Library, the humans have managed to infiltrate the Library as well and the race is on for the Index. The Arbiter enters the Library and reaches the Index, but finds Commander Keyes and Sgt. Johnson already there with the Index in hand. Sgt. Johnson begins to escort Keyes out when the Arbiter rushes in with his stealth technology activated, knocking out Sgt. Johnson and disarming Keyes. Just as he begins to get into position to get the Index, Tartarus captures her and takes the Index. As Tarturus tells him that he will die along with the rest of the Elites, he also says that the Prophets ordered him to kill the Arbiter. Then Tarturus sends the Arbiter off the edge of the floor into a pit with his war hammer...

The Chief slowly regains consciousness and finds himself and the Arbiter captured by a creature that can speak. Nearby is another monitor, 2401 Penitent Tangent, and the Prophet of Regret, both captured. The creature tells them that the monitor's containment procedure and the Covenant's Great Journey are the same; they both lead to a doomed existence. In order to stop it, they must unite to find the Index before it is activated. The Chief is teleported to the Sanctum of the Heirarchs, right in the middle of a broadcast the Prophet of Regret was doing. Outside, several Grunts and Jackals are revolting. As the Prophets flee, the Chief puts Cortana in the Covenant system to monitor activity while he tracks down the Prophets. While he fights his way through revolting Covenant, the Chief nears the Prophets but is interrupted by the slipspace rupture of In Amber Clad, that has been taking control of by the Flood. As he nears, Keyes and Sgt. Johnson are split up in different Phantoms. Suddenly, some popcorn Flood appear and one of them manages to cling onto the Prophet of Mercy's throat. Tarturus goes to help him, but Truth says let him be...

The Arbiter finds himself teleported to a location on Halo in the cliffs near a building. As he arms himself, he see's several Elites dead, killed by Brutes. Gathering what remains of the Council, the Arbiter leads the fight as they push deeper and deeper into the area. He reaches a beach, seeing the Elite he met outside the Library. The Arbiter tells him the Brutes have killed the Council. Two Phantoms show up, one bearing Keyes and the other Sgt. Johnson. A phantom drops off Tarturus and Keyes at a platform on the building, guarded by several Brute Honor Guard...

The Chief walks to the still-breathing Prophet of Mercy and asks him where Truth went. He says he went to Earth, to finish what they started. Cortana then points out that the object in the middle of the city is a Forerunner ship and Truth is taking it and the Covenant fleet to Earth. Cortana stays behind to make sure the Halo ring isn't activated. Behind them, a pelican crashlands and several Flood run out from the wreckage. The Chief then starts to backtrack to find a way to the Forerunner ship. As he reenters the buildings he was in, he finds that the Flood have already taken them over, infesting the very walls and fogging up the air inside. The Chief battles his way through, and Cortana informs him that several Flood are touching down all around the city. Finally, the Chief reaches a teleport and is being transported to the middle of the city at lightning speeds. The ship begins to take off and right before the teleport it cut off, the Chief shoots through the closing Forerunner ship doors and lands inside. The Forerunner ship then takes off and heads for Earth...

The Arbiter links up with the Elite and head towards a building. Outside, there's an unmanned scarab awaiting. As they get inside, the Arbiter rescues Sgt. Johnson and they team up to take out Tarturus. Sgt. Johnson takes the scarab to blow a hole in the doorway to Tarturus. The Arbiter escorts him to the building where the Council was supposed to watch the activation of the ring. As Sgt. Johnson blows open the door for him, the Arbiter goes inside and finds Tarturus. The Arbiter then tells 343 Guilty Spark to reveal to Tarturus Halo's true purpose; to destroy all life in the galaxy. Tarturus refuses to listen and forces Keyes to put the Index in its slot. As the ring is preparing to fire, several Elites and the Arbiter battle Tarturus. He is killed and Keyes manages to take out the Index before Halo is activated, canceling the fire sequence. Guilty Spark then tells Keyes and Sgt. Johnson that all the other remaining 7 rings have gone to stand-by status, which can only be activated by the Ark, the ship Chief and Truth are in...

The Ark exits slipspace near Earth and the human fleet is desperately trying to fend off the Covenant fleet. The admiral orders the Ark to be fired upon since they don't know who's ship it is, but the Chief gets on the radio. The admiral asks what the Chief is doing on the ship, and the Chief simply replies, "Sir, finishing this fight."