On Alpha Halo there was a Flood Containment Facility that was used by the Forerunners to contain the Flood while studying them. It is also very likely that there were similar Flood containment facilities on the other Halo rings, as they were observed on Installation 05 when the Marine Forces and Covenant Forces clashed there to retrieve the Index.
Discovery
During the events of Halo: Combat Evolved, 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, lying. The facility turned out to be a Flood Containment Facility. The Covenant had released the Flood and then, realizing their mistake, had attempted - unsuccessfully - to re-contain them. The area soon was completely overrun by the Flood, as the freed Infected organisms continued to help even more Flood escape and multiply. This area was destroyed along with the rest of Installation 04.
In Game Combat
Alpha Halo's Containment Facility was secured initially by Covenant Forces, who, upon discovering 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 Guerrilla War, went to the facility with Sgt. Johnson and part of Fire Team Charlie on the assumption that it was a weapons cache; it was not. After losing two marines, the first squad with Captain Keyes and Johnson continued until they found a locked door, which they eventually got through. This door was probably the same door that the Covenant forces locked in order to contain the Flood outbreak. All team members were directly infected by the Flood except for Sgt. Johnson. 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 countless 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 remaining 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.
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 entire story.
Inside the facility a small 3-man Marine ,fire team was found. They were the only other marines to leave the main containment building besides Sgt. Johnson. They were found by the Chief, but they were killed by the Flood before Chief had time to talk to them.
After fighting back the Flood and making his way back to the surface, the Master Chief regrouped with what remained of Corporal Lovik's Second Squad and valiantly led them to the center of the swamp, fighting back Flood by the dozen. As he reached the center, the Monitor of the Installation, 343 Guilty Spark, who was patrolling the area with Sentinels in an attempt to contain the outbreak of Flood, came across the Chief and his Marines. Identifying him as a Reclaimer, he abducted him, teleporting the Chief away from the swamp into The Library to retrieve the Index.
Heretic Uprising
During the Heretic Uprising, The Arbiter came across a Flood Containment Facility which had been compromised by the Heretics. This explained the presence of Sentinels, which had previously been unexplained. The Sentinels at this facility were under the command of 343 Guilty Spark, who had escaped the Pillar of Autumn mere moments before it and Installation 04 detonated. The Flood at this Facility were presumably killed when the Facility went into free fall.
Other Appearances
Flood Containment Facilities appear in copious locations, namely the Threshold gas mine. It is also likely that there is a Flood containment Facility at each ring, as there was one on both Alpha Halo and Delta Halo; however, the one located on Delta Halo had a large Flood outbreak, spawning the Halo 2 campaign missions The Sacred Icon and Quarantine Zone as well as the Halo 2 multiplayer map Containment. Another map feature contained Flood, but rather than being a Containment Facility it is instead a part of the land that has been blocked off with a small Sentinel Wall, the Halo 3 map Isolation. The Halo 3 map Cold Storage is in a Cryogenic Containment Facility located on Delta Halo.