At this point, the Chief is snatched up by Halo's quirky monitoring A.I., Guilty Spark. Spark, who refers to the Chief as "The Reclaimer," tells him that the Flood must be stopped and the only way to do so is to activate Halo's defense system. Spark explains that the Halo is a facility built by a long dead race known as The Forerunner. It was created to study and contain the Flood. Apparently there was a Flood outbreak long ago that was taken care of by the Halo's "contamination protocol". Spark is convinced this protocol is the only way to stop the current outbreak.
With Guilty Spark as his guide, the Chief fights his way through hordes of Flood to retrieve the Index, an ancient key needed to unlock Halo's defenses. After battling his way between Covenant and Flood forces, the Chief returns to the control room to activate Halo.
Once again, Cortana intervenes. Cortana explains to the Chief that he has been misled by Spark. If the Chief activates the Halo, he will destroy all the life in the galaxy. He learns that it isn't that the Halo holds a weapon; the Halo is a weapon. The Halo fires a massive pulse into space that wipes out all organic life that is capable of acting as a host to the Flood -- humans, Covenant, squirrels, everything.