The series starts out with the spaceship, UNSC Pillar of Autumn, emerging from slipspace. The main character, Master Chief, is called to action and given an artificial intelligence, known as Cortana. The ship is then under attack by an alien group, known as the Covenant. Master Chief then evacuates the ship to protect the A.I. He lands on the surface of Halo, a ring world. The men in the escape pod had all died, except for Master Chief. Chief and Cortana then meet up with other survivors, knownly Sergeant Johnson, of the Pillar of Autumn. They learn that the captain of the ship was captured by the Covenant. Chief and the survivors go on a rescue mission for Captain Keyes. Keyes orders Chief to get to the control center of Halo before the Covenant do. When they do, Cortana taps into the system and sends Master Chief to go back to Keyes urgently. Keyes thought they were going to find a weapons cache, but instead released an alien parasitic race known as the flood. Chief reaches Keyes, but finds signs of battle and a recording of the Flood. After this, a monitor known as 343 Guilty Spark appears and makes Master Chief grab something, known as the Index. It is shown that the Index is used to activate Halo and prevent the Flood from spreading. When they prepare to use the Index, Cortana appears to tell Chief that Halo is a weapon that will kill all sentient life in the galaxy. With this, Cortana and Chief decide to destroy Halo, through the self-destructing Pillar of Autumn. The two return to Keyes, to find that he had been infected by the flood. Chief grabs the neural implants in Keyes and activates the Pillar of Autumn's self-destruction sequence. 343 Guilty Spark then deactivates this and Chief has to manually destabilize the fusion reactors in the ship. Cortana and Chief escape the Halo as it is blown up. There is a bonus in the Legendary ending where Sergeant Johnson and an Elite are fighting. As the Pillar of Autumn blows up, the Elite and Johnson hug, knowing they are going to die. This bonus ending does not affect Johnson's role in the next game.
The game opens up to the trial of an Elite, an alien that is part of the Covenant. The Elite is named Thel 'Vadam. He is stripped of his rank as commander as he failed to stop Master Chief and the humans from destroying Halo. The Elite is then tortured by the commanding Brute, Tartarus. The setting shifts to Master Chief and Sergeant Avery Johnson, a UNSC sergeant that was part of the destruction of the Halo, being recognized for their actions at Halo. As they are being rewarded, a Covenant fleet appears and starts to attack the space station above Earth. Cheif and the humans aboard the station fight off the Covenant and learn that an important member of the Covenant heirarchy is in a cruiser attacking New Mombasa, Kenya. Cheif heads down to Earth to clear out the Covenant, in which the Covenant cruiser retreats and slipspace jump, with Chief, Sergeant Johnson, Miranda Keyes, and Cortana following on a UNSC ship. They find another Halo installation, and Chief is sent to kill the important member of the heirarchy, Prophet of Regret, while Keyes and Johnson find the Index for that installation. The story shifts back to the tortured Elite as he is dragged to the hierarchy's chamber. The hierarchy give him a position of Arbiter, so that he can fight for the Covenant. He is then sent on a mission to kill the Heretic, a group of Elites that rebelled against the Covenant knowing what the Halos can do. The Arbiter finds 343 Guilty Spark and brings him back to the Covenant. 343 Guilty Spark lead the Covenant to the Installation 05, the Halo that the UNSC discovered. Meanwhile, Chief fights through the Covenant forces that are protecting the Prophet of Regret. Soon after Chief kills Regret, the Covenant forces that 343 Guilty Spark lead to the installation arrives and attacks on Chief's position. With nowhere to go, Master Chief jumps into a lake and is rescued by a tentacled creature. After the death of the Prophet of Regret, the 2 other prophets decide to replace the Elite Honour Guards with Brutes. The Arbiter is sent on another mission to retrieve the Index. Keyes and Johnson gets the Index, but is confronted by the Arbiter. The Arbiter takes the Index from the humans, then is betrayed by the brute commander, Tartarus, and the Covenant. The Covenant Hierarchy had kicked out the Elites out of the Covenant because of their failure. The Arbiter is then thrown off the cliff, being saved by the tentacled creature, while Tartarus returns to the Prophets with the Index. The tentacled creature is named Gravemind, leader of the flood on Installation 05. Gravemind reveals the Covenant's quest will kill the Flood, humans, and the Covenant. The creature then sends Master Chief and Arbiter to different locations. Chief is teleported to High Charity, Covenant capital city. There, the UNSC ship that Miranda Keyes was on, crashes into the city. The ship is infested with the flood and spreads, killing the Prophet of Mercy, as the last remaining Prophet leaves to activate the ring with Keyes, Johnson, 343 Guilty Spark, and Tartarus. Chief follows Truth on a Forerunner ship, as Cortana stays behind to destroy High Charity and Halo, if the Covenant succeeds. Meanwhile, the Arbiter is teleported to the surface on Halo, regrouping with his fellow Elites. Arbiter and the Elites team up with Sergeant Johnson to get to the Control room. Tartarus activates the ring and the Arbiter and Johnson battle the Brute. They manage to defeat him, while Keyes is able to retrieve the Index to deactivate Halo. In doing so, they learn, through Guilty Spark, that the Installation were put on standby, and the only way to activate the Halos is through a location known as "the Ark." Master Chief's ship arrives to Earth, and is questioned by a commanding officer, what he is doing on the ship. Chief responds, "Sir, finishing this fight." In the Legendary ending, Gravemind is on High Charity, in which he asks Cortana questions. Cortana agrees to answer Gravemind's questions.
"The Master Chief crashes in eastern Africa, where he is found by Johnson and the Arbiter. The Chief, Johnson, and company fight Covenant in the jungle and arrive at a UNSC outpost. Here, Keyes and Lord Hood plan a final effort to stop the Covenant leader, the High Prophet of Truth, from activating a Forerunner artifact uncovered outside the ruins of the city of New Mombasa. The Chief clears anti-air Covenant defenses so Hood can lead the last of Earth's ships against the Prophet, but Truth activates the buried artifact, creating a slipspace portal which he and his followers enter. A Flood-infested ship crash-lands nearby; Elite forces arrive and vitrify Flood-infected areas of Earth, stopping the threat. Following a message Cortana left aboard the Flood ship, the Chief, Arbiter, Elites, Johnson, Keyes and their troops follow Truth through the portal. Joining them is 343 Guilty Spark, who aids the Chief as he has no function to fulfill after the destruction of his ringworld. Traveling through the portal, the humans and Elites discover an immense artificial structure known as the Ark, far beyond the edges of the Milky Way galaxy. Here, Truth can remotely activate all the Halos. The Flood arrive aboard High Charity in full force, beginning to infest the installation. Truth captures Johnson, as he needs a human to use Forerunner technology. Keyes is killed attempting a rescue, and Johnson is forced to activate the rings. Gravemind forges a truce with the Chief and Arbiter to stop Truth. The Arbiter, Master Chief, and Flood forces arrive and overwhelm Truth's guards, rescuing Johnson and halting the installations' activation. After the Arbiter kills Truth, Gravemind turns on the Chief and Arbiter. The Chief, Arbiter and Guilty Spark discover that the Ark is constructing another Halo to replace the one that the Chief previously destroyed. The Chief decides to activate this Halo; the ringworld would eliminate the Flood infestation on the Ark while sparing the galaxy at large from destruction. To activate the ring, the Chief rescues Cortana, who has the Activation Index of the destroyed Halo, from High Charity and destroys the city. Arriving on the new Halo, Cortana warns that Gravemind is trying to rebuild itself on the ring. The Chief, Arbiter, and Johnson travel to Halo's control room to activate the ring. Guilty Spark explains that because the ring is not yet complete, a premature activation will destroy it and the Ark. When Johnson ignores his warning, Guilty Spark fatally wounds him to protect "his" ring. Although the Chief destroys Guilty Spark, Johnson soon dies of his injuries. Chief activates the ring, and escapes the ring's self-destruction on the UNSC frigate Forward Unto Dawn. However, the force of Halo's blast causes the slipspace portal to collapse, resulting in only the front half of Forward Unto Dawn, carrying the Arbiter, making it back to Earth. A memorial service is held on Earth for the fallen heroes of the Human-Covenant war, during which the Arbiter and Lord Hood briefly exchange words regarding the fallen Master Chief. After the memorial service, the Arbiter and his Elite brethren depart for their home planet, Sanghelios. Meanwhile, the rear half of the Forward Unto Dawn drifts in unknown space. Cortana drops a distress beacon, but acknowledges it may be many years before they are rescued. The Chief enters cryonic sleep, telling Cortana to "wake me, when you need me." If the game is completed at the Legendary difficulty level, the scene continues to show the piece of Forward Unto Dawn drifting towards an unknown planet, revealed in the sequel to be known as "Requiem", the primary setting of the campaign of Halo 4."
"Four years after the events of Halo 3, UNSC Forward Unto Dawn drifts towards Requiem from the destroyed ring. Cortana wakes Master Chief from cryonic sleep shortly before rogue post-war Covenant forces board the vessel. The remnants of Forward Unto Dawn are caught in Requiem's gravity well and pass through an opening to crash-land on its interior. As Chief and Cortana explore Requiem, fighting hostile Covenant and mechanical warriors called "Promethean Knights", Cortana malfunctions. She reveals that she is experiencing "rampancy", a declining mental state where AIs past their operating expectancies "think" themselves to death. Chief promises to get Cortana to Earth, believing that Cortana's creator, Doctor Catherine Halsey, can fix Cortana's condition. Chief and Cortana pick up garbled transmissions from a human ship, UNSC Infinity, who have picked up Dawn's distress call. Cortana attempts to warn Infinity away from Requiem's gravity well and directs the Chief to deactivate what she believes are communications jammers. Instead, the Chief unwittingly releases the Didact, an ancient Forerunner warrior, from imprisonment. The Didact takes control of the Prometheans and Covenant, and attacks Infinity after it is dragged into Requiem. Chief makes contact with Infinity and helps repel the Didact's attack. Chief and Cortana recommend attacking the Didact while he is vulnerable, but Infinity captain Del Rio orders them to destroy the gravity well so their ship can escape. In the process, Chief is contacted by a Forerunner known as the Librarian—the wife of the Didact, as well as ancient humanity's protector. She explains that the Forerunners were divided on how best to combat the Flood. After failing to discover a way to immunize biological beings from the parasite, the Didact used a device called the Composer to convert the warriors under his command into mechanical Promethean Knights immune to infection. Requiring more soldiers, the Didact forcibly converted captured humans into Prometheans, before being stopped and imprisoned by the Librarian. The Librarian, who has guided humanity's development, accelerates the Chief's evolution; this grants him immunity to the Composer. After destroying the gravity well, Del Rio orders a retreat back to Earth, doubting the Chief and Cortana's testimony. The Master Chief disobeys orders to stand down and relinquish the malfunctioning Cortana, and stays behind to oppose the Didact. Infinity executive officer Commander Lasky gives Chief an armed transport and wishes him luck. Chief and Cortana attempt to sabotage the Didact's ship before he leaves, but when they are unsuccessful they follow the Didact to a Halo ring, Installation 03. The Composer has been moved from the ring onto the nearby Ivanoff Research Station, which the Covenant attack. The Chief defends Ivanoff, but the Didact retrieves the Composer and uses it on the station, composing every individual except the Chief. Chief and Cortana use a fighter to follow the Didact's ship through slipspace towards Earth. Aided by Infinity, now commanded by Lasky, and the UNSC home fleet, the Chief boards the Didact's ship with a nuclear warhead. Cortana inserts copies of herself into the Didact's computer systems to overwhelm the Didact's shield, but not before the Didact directs the Composer at Earth. With the help of Cortana, the Chief defeats the Didact, who falls into a slipspace portal generated underneath the Composer. The Master Chief activates the bomb but is saved by Cortana, who sacrifices herself. The Chief is found by a UNSC rescue team and is taken back to Infinity, where he, mourning the loss of Cortana, talks with Lasky about Earth, humanity, and what his duty as a soldier means. In a post-credits cutscene, UNSC forces descend on the city of New Phoenix, the location the Didact used the Composer on, to find its inhabitants composed. In a narration, the Didact proclaims the Forerunner's role as custodians of the galaxy having to bear the Mantle of Responsibility, and humanity as the greatest threat in the galaxy. Master Chief removes his armor aboard Infinity; if the player completes the game on Legendary difficulty, the Chief's eyes are briefly shown."
"Fireteam Osiris is deployed to the Covenant-controlled planet of Kamchatka to retrieve the rogue Dr. Halsey, who claims to have information on a series of devastating attacks on several human worlds, during a battle between Covenant forces and the Prometheans. While the team is successful in retrieving Halsey and eliminating the Covenant leader Jul 'Mdama, Halsey informs them that a new threat is about to emerge. Elsewhere, the Master Chief leads Blue Team on a mission to secure a derelict ONI research station known as Argent Moon. The arrival of a Covenant fleet forces Blue Team to scuttle the station instead. During the sabotage, the Chief receives a cryptic message from Cortana, directing him to the planet Meridian. John is ordered to return to Infinity upon destroying Argent Moon, but he and Blue Team disobey orders and set out after Cortana, forcing Captain Lasky to list the rogue Spartans as AWOL. This causes consternation aboard Infinity, as Halsey believes that Cortana's survival through the use of Forerunner technology makes her unpredictable and untrustworthy. Lasky gives Fireteam Osiris the aim of finding and capturing Blue Team. Osiris is deployed to Meridian to pursue Blue Team, where they find a human colony under attack by Promethean forces. During their pursuit, they encounter the Warden Eternal, a Promethean serving as Cortana's enforcer. After temporarily defeating the Warden, Osiris catches up to Blue Team, ordering them to stand down and return to Infinity. Blue Team, instead, board a Guardian: large Forerunner constructs built as enforcers of entire worlds. Osiris barely escape the colony's collapse as the Guardian activates and disappears. The Guardian emerges on the Forerunner planet Genesis, where John and Cortana reunite. Cortana says her terminal rampancy was cured by the same Forerunner technology that saved her. Osiris is deployed to the Sangheili homeworld of Sanghelios, where they plan to use a dormant Guardian that resides there to travel to Blue Team's location. However, the planet is engulfed in civil war; the remaining forces of the Covenant have chosen to make their last stand there. To hurry their mission, Osiris joins forces with the Arbiter and help him strike a crucial blow at the Covenant remnant. Osiris boards a Guardian with the help of Commander Palmer while the Arbiter finishes off the last Covenant troops. On Genesis, Osiris encounters the planet's caretaker, the artificial intelligence 031 Exuberant Witness, who allies with them to stop Cortana. Osiris catches up to Blue Team, who reveal Cortana is planning on using the Guardians to achieve galactic peace through forcible disarmament. Master Chief, aware of the massive devastation Cortana's plan will cause, attempts to convince Cortana to stand down. She refuses and confines Blue Team in a Forerunner prison, to prevent them from interfering with her plan. Osiris manages to transfer control of Genesis back to Exuberant, who wrests the prison from Cortana as she leaves the planet via a Guardian. Artificial intelligences across the galaxy begin swearing allegiance to Cortana and her plans. Cortana locates Infinity and prepares to disable it, but Lasky has the ship's AI Roland, who is still loyal to Infinity, engage slipspace away from Earth and commit to random jumps until they can develop a way to combat Cortana. With Blue Team recovered, Osiris returns to Sanghelios to reunite the SPARTAN-IIs with an injured Commander Palmer, Thel'Vadam, and Halsey. If the player completes the game on Legendary, an extra cutscene shows an unknown Halo installation powering up while Cortana hums, before cutting to black."