Flood containment facility

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.

In Game Combat
Alpha Halos' Containment Facility was secured initially by Covenant Forces, who, upon discoverin the Flood, were massacred and forced to lock down the facility. In the ensuing melee, (what appears to be) all Elites were either killed or infected, with only a few lances of Grunts and Jackals remaining. Later, Captain Keyes, in desperate need of weapons to arm his troops for their potentially long Guerilla War, went to the facility with Sgt. Johnsons squad on the assumption that it was a weapons cache. Needless to say, the routine recovery mission was tossed into utter chaos, with both human and Covenant forces being destroyed by the horrors that had been imprisoned for endless centuries.

By the time the Master Chief arrived at the location, the initial battle was over, with the remaining Covenant forces scattered and disorganized and the remaing Human forces holed up in the entrances, lashing out at anything that came near. The Flood itself, as if sensing a potentially new victim, quietly withdrew to the hole in which they sprang and prepared to attack their new enemy, leaving only hideous remains of their earlier killing spree to intimidate this new foe.

After the Master Chief made his way through the swamp and into the Facility, he encountered scattered Covenant, grisly remains of a terrible battle, a crazed Marine who was scared out of his mind, and a single recording chip that told the whole story.

After fighting back the Flood and making his way back to the surface, the Master Chief regrouped with what remained of 2nd Squad and valiantly led them to the center of the swamp, fighting back Flood by the dozens. As he reached the center, the Monitor of the Installation, 343 Guilty Spark, was patrolling the area with Sentinels, attempting to contain the outbreak of Flood, came across the Chief and his Marines. Seeing him as a good candidate as a Reclaimer, he abducted him, teleporting the Chief away from the cursed swamp of Flood.

Although the Master Chief did his best to save the Marines, only three survived to get to the Pelican. This is a heavy weight on the Chiefs mind.