The game begins as Pillar of Autumn exits slipspace and discovers a large alien ringworld of unknown origin. The Covenant pursue Autumn and heavily damage the ship. Autumn's captain Jacob Keyes entrusts the ship's artificial intelligence (AI) Cortana to the Master Chief to prevent the Covenant from discovering the location of Earth. Chief, Cortana, and the ship's surviving crew escape to the ringworld's surface while Keyes crash-lands the ship on the ring. On the ground, Master Chief and Cortana rescue other survivors. Learning Keyes has been captured by the Covenant, Master Chief infiltrates the Covenant cruiser Truth and Reconciliation to rescue him. Keyes reveals that the Covenant call the ringworld "Halo", and they believe it to be a weapon. Intent on stopping the Covenant from using Halo, Master Chief and Cortana fight their way to the ring's control room. Cortana enters Halo's computer systems. She sends Master Chief on an urgent mission to find and stop Keyes, who was looking for a weapons cache.
Reaching the captain's last location, Master Chief encounters a new enemy, a parasite that assimilates human and Covenant alike called the Flood. The release of the Flood prompts Halo's caretaker, the AI 343 Guilty Spark, to enlist Master Chief's help in activating the ring's defenses. After Master Chief retrieves the ring's activation index and prepares to use it, Cortana reappears. She has discovered that Halo is designed to wipe the galaxy of the sentient life that the Flood use as hosts, thus starving and destroying the parasite.
Defying 343 Guilty Spark, who sends his robotic Sentinels to stop them, Master Chief and Cortana decide to destroy Halo to prevent its activation or the escape of the Flood. Needing Keyes' command codes to destroy Autumn and Halo with it, Master Chief returns to Truth and Reconciliation, only to find Keyes assimilated by the Flood. Retrieving the codes from the captain's remains, Master Chief returns to Autumn, but the self-destruct sequence is stopped by 343 Guilty Spark. Master Chief and Cortana manually destabilize the ship's reactors instead, narrowly escaping the blast in another ship
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