The Flood are unleashed.
When Keyes and a squad of Marines fall prey to the Flood, the Chief discovers yet another artificial intelligence—343 Guilty Spark, the resident monitor of Installation 04. This bizarre new construct guides SPARTAN-117 to a solution against the parasitic threat, where he discovers that upon retrieving an object known as the Index, he can activate Halo's defenses and destroy the Flood.
Before he can pull the trigger, however, Cortana stays his hand and explains that the Halo installation was not the weapon they had once thought it to be. By activating Halo, he would not only destroy the Flood, but also every sentient creature in the galaxy. Since there was no way to attack the Flood directly, the installation was designed to starve it to death by killing what it needed to survive.
With Halo's activation Index in hand, the Chief and Cortana rushed to the Pillar of Autumn for what seemed to be the only effective solution—destroy Halo. Using the ship's reactors, they detonated the engine's fusion core, creating an explosion so powerful that it broke the ring apart.
With no apparent survivors, the Master Chief and Cortana made their way home.