This game is REVOLUTIONARY!!!!
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 has 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. The Master Chief (left) converses with 343 Guilty Spark (right).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 small starship before Halo explodes. The ending reveals that 343 Guilty Spark survives the explosion of Halo, and the story is continued in Halo 2.