 Dropped into the swamp where Keyes and his squad disappeared, the Master Chief discovers that the Captain has been captured and both human and Covenant soldiers have been turned into zombie-like creatures by bulbous aliens. One soldier, Private Wallace Jenkins, is left still semi-conscious and painfully aware of his predicament, unable to control his movement or actions as his former friends and he attack McKay's troops. Jenkins intends on ending his life, but is instead captured by McKay for study. The Chief is approached by Halo's resident A.I., 343 Guilty Spark, who informs the Chief that the creatures he has encountered are called the Flood, a virulent parasite that infects hosts and converts them into either forms for combat, or for reproduction. To activate Halo's defenses, Guilty Spark needs the Master Chief's help. In Halo's Control Room, Guilty Spark gives the Master Chief the key to activate Halo, but is stopped by a furious Cortana. Cortana explains that Halo is a weapon, but it doesn't kill the Flood- it kills their food, meaning humans, Covenant, and any other sentient life. Realizing that they have to stop Guilty Spark from activating Halo, Cortana and the Master Chief decide to destroy Halo by detonating the crash-landed Pillar of Autumn's fusion reactors. In order to do this, they need Captain Keyes' neural implants. Cortana discovers the Captain is still alive, held prisoner once again aboard the Truth and Reconciliation, now in the hands of the Flood who are trying to escape Halo. The Chief fights Covenant and Flood to the Captain, but finds out he is too late — the Captain has been assimilated into the parasite. The Chief retrieves the implants and leaves the Truth for the Autumn.
