The UNSC Pillar of Autumn arrives at Installation 04 after fleeing the planet Reach, only to find a Covenant fleet waiting for them. The ship and crew crash-land onto the Halo, and in the process of trying to investigate the purpose of the ring-world, release the Flood, an ancient biological weapon. In order to stop the Flood and keep the Halo from firing and killing everything in the galaxy, Master Chief and Cortana detonate the Pillar of Autumn's reactors, breaking the Halo apart.
Halo: The Flood follows the events of the crew of the UNSC Pillar of Autumn on the surface of Alpha Halo in September 2552.
The Flood primarily follows John-117 and Cortana’s actions during the Battle of Installation 04.
The Flood tells the final chapter in the story of the UNSC Pillar of Autumn, ending in a self-destruction of the ship’s reactors, destroying the ship and Alpha Halo.