On Alpha Halo there was a Flood Containment Facility that was used by The Forerunners to contain the Flood while studying them.
Discovery
During the events of Halo 1, UNSC forces, led by Captain Jacob Keyes, attempted to take a Forerunner facility hidden in a swamp. A Covenant Elite named 'Qualomee told them that it was a weapons cache. The facility turned out to be a Flood Containment Facility. The Covenant had released the Flood and then, realising their mistake, had attempted - unsuccessfully - to recontain them. The area soon was completely overrun by the Flood, as the freed organisms continued to help even more Flood escape and multiply. This area is presumed destroyed along with the rest of Installation 04.