During the combat with the Covenant, we find an even more frightening enemy. The Flood. A parasitic organism that will kill and infect any sentient life-form it comes across. It's whole purpose? To control and consume. It is nearly unstoppable and requires massive amounts of both nerves and firepower to engage these nightmares. The Halo construct was designed to eliminate the Flood by destroying all sentient life in the Universe, thereby starving it out. The only way to end both the threat of the Flood and the installation to the rest of the galaxy, was to destroy Halo.
Now the real battle begins. The fight on Earth is brief, but intense. With the Covenant forces defeated, the High Prophet Regret immediately retreats. The UNSC ship, In Amber Clad, follows them. Once out of slipspace, they find a second Halo ring. Obviously the first one, was not the only. Master Chief is sent to kill Regret, while the crew searches for how to destroy the second installation.You also take part as the Elite warrior, Arbiter, to learn about the Covenant side of story. You learn the Prophets have lied to them for generations and mean to betray all the Elites.
While traveling on this newest Halo, you encounter the Gravemind, the collective consciousness of the Flood. His goals mirror your own, although for more selfish reasons. He sends Master Chief to High Charity to take advantage of a Covenant civil war. This was used as a distraction so the Gravemind could infest In Amber Clad and spread the flood. The High prophet of Mercy is taken by the flood forms once they escape the ship. Unable to destroy Halo and prevent the sequence firing, they yank the Index, causing the system to prime all the rings so they can only be fired from The Ark. Cortana stays behind to destroy the Flood infested ship, High Charity.
The Covenant have discovered the portal to the Ark in Africa. Master Chief is sent in to take it back before the Covenant can get to it. During the fight, a flood infested ship arrives and starts taking over as much as it can, before your new found allies, the Elites, start eradicating the infestation. You and the Arbiter, along with Forward unto Dawn, chase the High Prophet Truth, and his forces through the portal.
Spartans never die.