Halo 3 Storyline

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The storyline begins several weeks after the events of Halo 2. SPARTAN-117 enters Earth's atmosphere and crash lands in an east African jungle. After being retrieved by Sergeant Major Avery Johnson, the Arbiter, and a handful of Marines, the group makes their way through the jungle toward a designated extraction point. Covenant forces are sighted in the area and Johnson makes a strategic decision to split the group up to reduce their chances of getting spotted. SPARTAN-117 and the Arbiter continue on their way to the extraction zone with the second squad, fighting off numerous Covenant troops in the process, but upon reaching the extraction zone, Avery Johnson's Pelican group consisting of two Pelicans, are ambushed and shot down by Banshees. Johnson and his men are then captured and taken prisoner by a number of Brutes led by a Gravity Hammer-wielding Chieftain. The Master Chief, Arbiter, and company fight their way through hordes of enemies and eventually rescue them, after which a Pelican arrives and picks them up.

The Pelican brings them to Crow's Nest which is used as a local base of operations by the UNSC. Here, Commander Miranda Keyes and Lord Hood plan a last-ditch effort to stop the Covenant from activating a Forerunner artifact uncovered outside the ruins of the city of New Mombasa. Their plan is to have the Master Chief with a small group of marines to punch a hole in Truth's anti air defense, so that Lord Hood can initiate a low level strike on the artifact. Their planning is quickly interrupted when power is cut and the Prophet of Truth broadcasts an announcement to all surviving human forces that their doom is inevitable. Soon after that, the Covenant Loyalist discovers the facility and mount a heavy assault. After a brief struggle, the outpost is lost and is blown by a bomb activated by SPARTAN-117. Deep underground, the Master Chief regroups with the surviving Marines and makes his way into the African City of Voi, Kenya via the Tsavo Highway. Shortly afterwards, SPARTAN-117 along with a handful of Marines destroy all Covenant anti-air defenses so that Lord Hood can lead the last of Earth's frigates against Truth and the artifact. As Hood mounts his attack on Prophet, Truth activates the artifact and creates an enormous slipspace portal, into which all the Covenant ships retreat.

At the same time, a Covenant cruiser controlled by the Flood, a parasitic species, had broken through the Elite's Quarantine of High Charity and arrived suddenly via slipspace and crashes into Voi, and the parasite quickly spreads throughout the entire city. As the Human forces attempt to fight the infestation, many are infected by the Flood. The Covenant Separatists lead by Shipmaster Rtas 'Vadum, arrives at Earth and assists the struggle against the infestation. The Elites inform Commander Keyes that a UNSC construct is aboard the crashed Flood ship, and identified it as Cortana. After retrieving Cortana, SPARTAN-117 returned to the Shadow of Intent to oversee the repairs made by 343 Guilty Spark. However, it is only a recorded message from her. Cortana informs that the Gravemind is coming to Earth with an army of Flood, and that on the other side is a solution to the Flood infestation, without having to fire the rings. Lord Hood questions Cortana's plan, assuming that it could be a Flood trap, but SPARTAN-117 firmly tells Hood that he trusts her.

Lord Hood remained on Earth to defend it against the incoming Flood invasion while Commander Keyes and the Elites journeys through the Portal. Arriving at the Ark, the Covenant Separatist engages on the Covenant Loyalist fleet while the UNSC launches a ground campaign. After landing on the Ark, 343 Guilty Spark helps lead Master Chief and UNSC forces to the Ark's Cartographer, the map room of the Ark, to locate the Control Room of the Ark. In order to access the Control Room, the UNSC and the Covenant Separatists must deactivate three shield generators which are inside three separate towers. While SPARTAN-117 and the Arbiter succeed in deactivating the first and second towers, Johnson radios Keyes, telling her that he must retreat due to the heavy enemy assault. When SPARTAN-117 and the Elites arrived to the third tower, Johnson and his men are nowhere to be seen. After the final shield barrier protecting the Control Room deactivates, the Flood-infested High Charity arrives via slip-space and crashes onto the Ark, releasing Flood Dispersal Pods as it falls. After handling with the nearby infestation, SPARTAN-117 leads the remaining UNSC and surviving Elite forces via armoured vehicles in an assault on the Citadel containing the Control Room, which is heavily defended by Covenant Loyalist forces. Once inside the Citadel, Truth broadcast his sermon and reveals the captured Johnson to his followers. Just as Truth is about to force Johnson to activate the rings, Keyes crashes into the Control Room using a pelican. Knowing she can't kill all of the Brutes, Keyes realizes that she must kill Johnson and herself to stop the rings from being activated. From behind, Truth fires several Spiker rounds at Keyes and then pushes Johnson's hand down on the Ark's terminal, activating all of the remaining Halos in the galaxy.

Just as SPARTAN-117 and the Arbiter reach the top, two Flood Tank Forms confront them. Gravemind, through the two Flood forms, urges the two to join forces in stopping the initiation of the Halos and Truth. With the Flood's help, SPARTAN-117 and the Arbiter slaughtered all the Covenant forces defending Truth. Upon arrival to the Ark's Control Terminal, they find Johnson mourning over Keyes' dead body, and Truth partially infected. The Arbiter, after a short confrontation with Truth over the truth of the Halos, executes Truth with his Energy Sword, while the Master Chief deactivates all the Halos. Shortly after the deactivation of the Halos, the Gravemind betrays them and prevent the duo from escaping.

The duo manage to escape from the Citadel via access hole near the elevator they used earlier. SPARTAN-117 then experience hallucinations of Cortana and follows the figure to a control panel. He then activated the panel, surprised to see that the Ark is manufacturing a replacement Halo in the event of one being destroyed. Knowing that the threat of the Flood is undeniably apocalyptic, SPARTAN-117 decides he will activate the new Halo. Needing an Index in order to fire the ring, SPARTAN-117 journeys into the crashed High Charity and fights against the Flood to retrieve Cortana (knowing that she still has the Index she acquired from Installation 04). Once retrieved, Cortana instructs the Spartan to overload High Charity's engines in order to destroy the Gravemind. The Arbiter arrives via Banshee to assist the Spartan in fighting the Flood. The two escaped from High Charity before it explodes using a damaged but still flyable Pelican.

The surviving Elites and UNSC personnel return to Earth, leaving only Sergeant Johnson, SPARTAN-117 with Cortana and the Arbiter to make their way to the new Halo. As they make their way to the new Halo's Control Room, Flood forms arrive via Flood Dispersal Pods to prevent the activation of the Halo. From here, they quickly discover that Gravemind is attempting to reconstruct itself on the new Halo. As Sergeant Johnson tries to activate the Halo, 343 Guilty Spark fires his defensive laser at him after realizing that it will destroy the installation. The Monitor then turns against the Spartan and blast the Arbiter out of the Control Room, leaving the Spartan to destroy Guilty Spark himself. SPARTAN-117 successfully destroys the Monitor with the Spartan Laser and tried to mend Johnson. Mortally wounded, Johnson urged the Spartan to send him out "with a bang". With the Halo activated, SPARTAN-117 and the Arbiter race towards the frigate Forward Unto Dawn using Johnson's Warthog. With no time to reach the cockpit, the Master Chief uploads Cortana into the frigate to start taking off before the Arbiter is able to take the controls. The front half of the Dawn, containing the Arbiter, makes it through the portal. However, as Halo shakes itself to pieces during its firing sequence and damages the Ark, the portal deactivates before the other half of the Dawn containing Chief and Cortana made it through.

Back on Earth, Lord Hood holds a memorial service in honor for those who died in the Human-Covenant War, with the Arbiter and many Marines in attendance. With Truth dead, the Covenant destroyed, and the Flood wiped out, the long and devastating war is finally over. Though he says he can never forgive the Arbiter for what the Covenant did to the human race, Lord Hood sincerely thanks him for standing by the Master Chief until the end. After the service, the Covenant Separatist returned to their home planet. Then, credits rolls.

After the credits, it is revealed that SPARTAN-117 and Cortana are still alive aboard the rear section of the Dawn, which had apparently torn off before going through the portal. The Spartan floats to a cryotube and as he climbs in, Cortana comments "I'll miss you." He replies "Wake me, when you need me."

If the last level is completed on Legendary difficulty, the section of Forward Unto Dawn that Cortana and the Chief are aboard is seen drifting towards an unknown planet.