The battle for the Ark.
After a series of battles in an effort to locate the Ark's control room, the Master Chief and the Arbiter finally reach Truth's location, barricaded within a towering citadel. Their arrival, however, is not without loss. Recognizing that only humans can fire the Halo installations, the Prophet of Truth kills Keyes, forcing Johnson to activate the rings.
As the process begins, the Ark's atmosphere is suddenly torn open and High Charity spirals down from the sky, crashing into the surface of the installation. The Flood had arrived.
With the assistance of the Gravemind, its motivations closely aligned to theirs, the Arbiter and the Chief laid siege to the control room. Here, the disgraced Elite finally exacts his revenge against the Covenant, killing the Prophet of Truth and stopping the rings from firing.
Though Johnson manages to escape, the truce between the Flood and humanity is short-lived. Both the Master Chief and the Arbiter are quickly assaulted by the Gravemind and forced to flee deeper into the citadel. During their escape, the true purpose of the Ark is finally revealed as an enormous ring rises from the foundries at the center of the installation.
Now becoming clear, the Chief and the Arbiter realize that the Ark is not only capable of firing the Halo installations, but also rebuilding them in the event that one is damaged. Knowing that this replacement was for the one he destroyed and that Cortana may still lie somewhere in High Charity, the Chief quickly realizes what he must do.