Halo
The story is presented through an instruction manual, scripted events and conversations during the game, and in-game cut scenes. The game begins as the Pillar of Autumn exits slip-space near a mysterious ring-shaped space station, called "Halo" by the Covenant. A Covenant fleet attacks and heavily damages the Pillar of Autumn. Jacob Keyes initiates "The Cole Protocol", a procedure designed to prevent the Covenant from learning the location of Earth. While Keyes prepares to land the ship on Halo, the Master Chief and Cortana escape via an escape pod, which crash lands on the ring.
Captain Keyes survives the Autumn's crash landing, but is captured by the Covenant. In the second and third levels of the game, the Master Chief and Cortana gather human survivors and rescue Captain Keyes, who then orders Master Chief to beat the Covenant to Halo's control center and to discover its purpose. The Master Chief and Cortana travel to a map room called the Silent Cartographer, which leads them to the control room. There, Cortana enters the systems and, discovering something urgent, suddenly sends the Master Chief to find Captain Keyes, while she stays behind. While searching for his commander, the Master Chief learns that the Covenant have accidentally released the Flood, a parasitic alien race capable of spreading itself by overwhelming and infesting other sentient lifeforms. Keyes falls victim to them while looking for a cache of weapons. The release of the Flood prompts 343 Guilty Spark to recruit the Master Chief in retrieving the Index, a device that will activate Halo and prevent the Flood from spreading beyond the facility.
After the Master Chief retrieves and begins to use the Index, Cortana re-appears and warns him against the activation. She has discovered that Halo's defense system is a weapon designed to kill all sentient life in the galaxy, thus effectively starving the Flood. When confronted with this information, 343 Guilty Spark states that the installation technically only has a maximum radius of twenty-five thousand light-years, but that its pulse would trigger other similar installations as well, killing all sentient life in the galaxy.
With Cortana's help, and while fighting the Flood, the Covenant, and Guilty Spark's Sentinels, the Master Chief attempts to destroy Halo before 343 Guilty Spark activates it. Cortana discovers that the best way to destroy Halo is to cause the crashed Pillar of Autumn to self-destruct. However, Captain Keyes' authorization is required to destroy the ship. By the time that they reach Keyes, he has been infested and turned into a Brain Flood. The Master Chief retrieves Keyes' neural implants directly from his brain, and Cortana activates the Autumn's self-destruct sequence. However, 343 Guilty Spark reappears and deactivates the countdown, discovering the record of human history in the process. The Master Chief manually causes the Pillar of Autumn's fusion reactors to begin to melt down, giving him and Cortana only fifteen minutes to escape. The Master Chief and Cortana flee in a UNSC Longsword fighter, before Halo explodes. The ending reveals that 343 Guilty Spark survives the explosion of Halo, and the story is continued in Halo 2.
Halo 2
The story of Halo 2 is told through in-game dialogue as well as cutscenes; the back-story to the game can be found in the game manual. Taking place shortly after the events of the novel Halo: First Strike, the game opens with the judgment and torture of a former Covenant Elite Commander, who is being punished by his fellow Covenant for failing to stop the destruction of the ringworld Halo during the events of Halo: Combat Evolved. This is juxtaposed with the recognition ceremony of the humans Master Chief and Sergeant Avery Johnson receiving awards aboard Cairo Station, a MAC gun platform orbiting Earth, alongside Commander Miranda Keyes. It is revealed that the Covenant's interest in Halo lies in the belief that the activation of Halo would bring about the "Great Journey", which would allow them to follow the ancient Forerunners to the "divine beyond".
Soon after the commencement of Master Chief's ceremony, a Covenant fleet jumps out of slipspace near Earth. The Covenant proceeds to send boarding parties towards a battle cluster of MAC stations. These boarding parties are secretly carrying explosives designed to take out the MAC (Magnetic Accelerator Cannon) guns that protect Earth from attack. Master Chief finds and disarms a bomb located on Cairo Station with the help of Cortana, while the flagship of the Covenant fleet speeds past Earth's defenses and heads toward Earth itself. Master Chief and Cortana join the UNSC ship In Amber Clad, which is en route to New Mombasa to deal with the Covenant flagship.
Before reaching New Mombasa, Cortana decodes transmissions revealing that the flagship carries the High Prophet of Regret, an important Covenant figure. The UNSC successfully repels the Covenant invasion force with the help of Master Chief, and the Covenant ship begins preparations for a slipspace jump to an unknown destination. The ship makes the jump, and the city is destroyed in the shockwave. To avoid destruction, In Amber Clad follows and discovers a second Halo installation dubbed "Delta Halo". Despite the Covenant's own ideas about the rings, Master Chief and the crew of the Amber Clad know that the rings are actually weapons that if activated would wreck devastation on a galactic scale. Master Chief is sent to kill the High Prophet of Regret while Keyes attempts to secure the Index to prevent the activation of Delta Halo.
Meanwhile, the disgraced Covenant commander has been given a chance to redeem himself as the "Blade of the Prophets", the Arbiter. His first mission is to silence a heretic who doubts the Prophets' teachings, in turn starting the Arbiter along a path which ultimately results in him doubting his own beliefs about Halo. Seeds of discord are further sown within the Covenant when the Prophets decide to grant the Brutes the job of protecting the Prophets instead of the traditionally favored Elites. During his missions, The Arbiter finally realizes the danger that the rings represent.
The Master Chief and the Arbiter meet upon the release of the Flood, a race of parasitic creatures, from Delta Halo. A mysterious Flood creature called the Gravemind sends the Arbiter and Master Chief in separate directions to prevent The High Prophets from activating Delta Halo. Master Chief finds himself aboard the Covenant Holy City High Charity, a gargantuan space station, and pursues the remaining Prophets. During his mission, he finds himself in the middle of an erupting Covenant civil war between the Brutes and the Elites. After capturing In Amber Clad, the Flood, led by Gravemind, arrive at the city and begin to consume and infect the populace. The only remaining High Prophet, Truth, escapes on a Forerunner vessel hidden in the core of High Charity. The Master Chief stows away on board while Cortana stays behind in order to detonate the In Amber Clad's engine reactors to destroy Delta Halo and High Charity if the Brute Tartarus activates the ring. The Arbiter, with the help of fellow Elites, Avery Johnson, and Keyes, manage to stop the firing. However, the unexpected shutdown causes the ring to send a signal out to the other remaining Halos, sending them all into a "standby" mode so they can be remotely activated from the Ark. Meanwhile, the Forerunner ship that Master Chief has stowed away on approaches Earth. One of Earth's remaining orbital forces contacts him and asks what he is doing aboard the Forerunner ship. He replies, "Sir, finishing this fight," ending the game with an abrupt cliffhanger and setting the tone for Halo 3.
