Intro to Halo 3

When the game begins, John-117 is back on Earth, where the Covenant Loyalists (Prophets, Brutes, Drones, Grunts, Hunters and Jackals), led by the Prophet of Truth, have laid waste to most of the planet. Humankind's population has been reduced to at least 200 million people, and is backed up against a wall, fighting for its very survival. The only reason that they have survived for this long is that the Covenant is preoccupied by an excavation site a few miles from the ruins of the East African city New Mombasa. There, they have uncovered a massive Forerunner structure, which is seen in the E3 2006 trailer, that has been buried under the planet's surface for thousands, if not millions of years. It was partially uncovered due to the Slipspace jump that was attempted in Halo 2 by the Prophet of Regret.

The Master Chief and the Arbiter in an African jungle.Sergeant Major Johnson, the Arbiter, and a handful of Marines retrieve Master Chief after a rough jump from orbit, landing in a section of the east African jungle. The group begin to venture to a designated extraction point until Johnson decides to split up with the Arbiter and the Chief to reduce their chances of getting spotted. Master Chief and the Arbiter continue on their way to the extraction zone until Johnson's Pelican is shot down by Banshees and later Johnson and his men are captured by Brutes. The Master Chief and the Arbiter fight their way through hordes of enemies and eventually rescue free Johnson and his men. A Pelican arrives to pick them up and flies away.

UNSC Underground Facility "Crow's Nest"The Pelican brings the three of them to The Crow's Nest, a 21st century facility used as a local base of operations by the UNSC. Shortly after they reach their destination, the Covenant mounts an attack on the facility. After a brief struggle, in which the outpost is lost, Master Chief receives orders from Commander Keyes to clear a way into the African city of Voi, and destroy all Covenant anti-air defenses in preparation for an all-out assault on Truth and the artifact. After the Master Chief and the Arbiter destroy the defenses, Truth activates the artifact and creates an enormous slip space portal, into which all the Covenant ships retreat. As Keyes follows the Dreadnought a Covenant ship controlled by the Flood arrives by slip space and crash lands nearby, and the parasite quickly spreads throughout the city of Voi.

The Elites inform Commander Keyes that a human construct is aboard the ship, and identify it as Cortana. The Master Chief and the Arbiter attempt to fight off the Flood and retrieve Cortana from the Flood ship. After they have completed all of their objectives, 343 Guilty Spark arrives by an Elite vessel, and insists that he take Cortana somewhere where he can make repairs, claiming that now his Installation has been destroyed he has no more preset functions, and wants to help the Master Chief destroy the Flood. Once the Arbiter and Master Chief are evacuated, the Elites glass the half of Africa. This amplifies the hard feelings between Lord Hood and Ship master Rtas 'Vadum, the Spec. Ops Leader of Halo 2, Shipmaster of the Shadow of Intent and Fleet Master of the Elites.

Guilty Spark manages to make efficient repairs to Cortana, but the Master Chief realizes it isn't her, but only a recorded message from her. The message states that through the portal that Truth retreated into is unknown to the Gravemind, and on the other side is a solution to the Flood infestation, without having to fire the rings. Lord Hood questions Cortana's plan, saying it could be a Flood trap, but the Master Chief firmly tells Lord Hood he completely trusts her.

Once the Elites and Lord Hood decide to follow Truth, the remaining Elite ships and UNSC Frigates (approximately 12 ships total) leave Earth via the slip space portal and find themselves near an immense artificial structure, which is soon revealed to be The Ark. Arriving at the Ark, they engage a Covenant fleet three times their size. After landing and fighting their way to the Cartographer of the Ark, the Master Chief and the Arbiter find out that the Ark is in fact positioned at the edge of the Milky Way, just beyond the Halo rings' effective firing range. The Monitor explains that the humans and the Elites must deactivate three shield generators, which are inside three separate towers, to access the Control Room of the Ark.

Upon arrival at the three generators, the Master Chief takes a squad to the first tower, The Arbiter takes his Elites to the second, and Sergeant Johnson takes another squad to the third. While Master Chief and The Arbiter succeed, Johnson tells Keyes that the fire is too heavy and he must retreat, so she tells the Arbiter and Master Chief to go and help him. On arrival to the third tower, Johnson is nowhere to be seen. The Master Chief and Arbiter kill the Brutes defending the tower and deactivate it. Just after the shield protecting the Control Room drops, the Flood-infested High Charity arrives by slip-space and crashes into the Ark, releasing Flood Dispersal Pods as it falls. 343 Guilty Spark insists that he assesses the damage that High Charity did to the Ark, so the Arbiter and Elites leave the humans to avoid Guilty Spark being captured by the Flood. The citadel containing the Control Room is defended by countless Covenant forces and two Scarabs. After all the forces are defeated, Guilty Spark and the Arbiter return, and they and the Master Chief enter the citadel. Once inside, they see that Truth has captured Johnson, knowing that only humans can activate Forerunner Installations, but are too far away to save him. Keyes commandeers a Pelican and crashes it in the Control Room, keeping the Brutes at bay with a Shotgun while tending to Johnson, but knowing she can't kill all of the Brutes there, she realizes she must kill Johnson and herself to stop the rings from being activated. She is about to shoot Johnson before Truth grabs a Spiker and shoots her several times in the back with it, killing her. Johnson is overcome with sadness and Truth is easily able to force his hand down on the Ark's terminal, activating all of the Halos in the galaxy.

The Master Chief and Arbiter take an elevator up to the Control Room, despite knowing it is too late. As they reach the top, two Flood Tank Forms confront them, but say that the only way to stop the Halos is by joining forces. With the Flood's help, the Master Chief and Arbiter kill all the Covenant forces defending Truth. Upon arrival to the Ark's terminal, they find Keyes dead, Johnson mourning, and Truth partially infected. After executing The Prophet of Truth before he can submit to the Flood and deactivating all the Halos, the Gravemind betrays them. Johnson attempts to escape with Keyes' Pelican, but the Gravemind prevents the Arbiter and Chief from escaping with him.

Johnson radios Chief, telling him to find another way out, so he and the Arbiter shoot their way back to the entrance elevator, but it is deactivated. Behind the elevator is a hole, leading to a lower level of the citadel. Cortana briefly shows herself to the Chief, and leads him to a control panel which reveals her plan - it releases a 'replacement' Halo in the event of one being destroyed. However, Guilty Spark tells them it will take quite some time to fabricate an Index needed to fire the Halo, but the Master Chief remembers that Cortana still has the Index that she acquired in Halo: Combat Evolved. He infiltrates the crashed High Charity, which is completely overrun by Flood. Cortana becomes rampant before the Chief can reach her, but Cortana is able to contain the functional part of herself in a stasis-field, where she waits. Master Chief breaks the stasis-field and retrieves a perfectly-functioning Cortana. She tells him to overload High Charity's engines in order to destroy the Gravemind. The Arbiter arrives via Banshee and helps the Chief fight the Flood. They find a Pelican, which had presumably crashed while humans were inside High Charity during Halo 2. Damaged but still flyable, the Master Chief uploads Cortana into the Pelican and flee High Charity before it explodes.

Cortana makes contact with Johnson, who safely made it back the Shadow of Intent. He tells her that he will land the frigate Forward Unto Dawn near Halo's Control Room, and will be ready to pick them up and head back to Earth after they activate the Installation. When they arrive on the newly built Halo, they quickly discover that Gravemind is attempting to reconstruct itself on the new Halo. The Chief, Arbiter, and Sergeant Johnson quickly make their way to the Control Room, where they attempt to fire Halo. Guilty Spark realizes that this will destroy his new ring because it is not fully ready yet, as well as the Ark, and shoots his defensive laser at Sergeant Johnson as he tries to activate the ring, critically wounding him. Master Chief destroys Guilty Spark with a Spartan Laser, but Johnson tells Chief to send him out "with a bang" and dies. Cortana activates Halo, and Chief takes Johnson's Warthog with the Arbiter and race towards the Frigate. 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, Halo shakes itself to pieces during its firing sequence and damages the Ark, deactivating the portal before the half of the Dawn' containing Chief and Cortana make it through.

Back on Earth, Lord Hood holds a memorial service in respect for those who died in the Human-Covenant War, with the Arbiter and many Marines in attendance. Lord Hood thanks the Arbiter for standing by the Master Chief until the end. After the service, Shipmaster tells the Arbiter that just like they have made sure the Human home world is safe, he wants to make sure the Elite home world is safe. The Arbiter tells him that with the eradication of the Covenant, they have made it so. He tells the piloting Elites to take them home, the credits roll.

After the credits, footage is shown of the Master Chief and Cortana on-board the rear section of Forward Unto Dawn, which had apparently torn off during the slip-space jump; the pair are drifting through space. Cortana tells the Chief she will drop a distress beacon, but that it could be years before they are found. The Chief floats to a cryotube, and as he is climbing in Cortana comments "I'll miss you." He replies "Wake me when you need me."

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

Halo 3 Levels
Levels in Halo 3 are as follows:

Arrival - Brace for impact. (No actual gameplay.)
Sierra 117 - Rise up. Start the fight.
Crow's Nest - Clear the base, whatever it takes.
Tsavo Highway - Mount up. Get to Voi.
The Storm - Reclaim the city. Make a hole.
Floodgate - Stop the infestation. Find Cortana.
The Ark - Search the waste for the Cartographer.
The Covenant - Breach the barrier. Stop Truth.
Cortana - Cleanse High Charity. Save Cortana.
Halo - Light the ring. Destroy the Flood. "Finish The Fight."