Outbreak at the Containment Facility

Several battles in the Containment Facility were the turning point of the UNSC and Covenant's involvement in the Battle of Installation 04, where the two sides proved unprepared for a third enemy: the Flood.

Prelude
Following the activation of the Halo Array at the end of the Forerunner-Flood war, the Forerunners kept samples of the Flood contagion in Flood containment facilitys spread across their installations for study. During the ongoing campaign for control of Installation 04 in September 2552, the Prophet of Stewardship dispatched secondary and tertiary artifact hunting groups to what was believed to be a Forerunner weapons cache. These teams encountered the Flood and fell silent, eventually leading the Prophet to send a fourth before Fleetmaster Thel 'Vadamee reprimanded the Prophet for misallocation of military resources.

While the upper levels were cleared, the lower levels were infested and some Sangheili commanders were lost in the process. During this time, a Sangheili warrior named 'Qualomee purported to deliver a cache of weapons to the Covenant troops in this facility, though he was eventually captured by UNSC forces and interrogated for hours in Alpha Base.

Despite the success of the Raid on the Pillar of Autumn conducted by Lieutenant Melissa McKay bringing much-needed supplies to fortify Alpha Base, Captain Jacob Keyes decided to personally lead a small force of Marines to investigate the supposed weapons cache. The marines were inserted by Pelican dropship into the swamps surrounding the facility, and proceeded to make their way inside on foot.

The raid
Pelican Victor 933 was the first Pelican dropship to arrive in the area, though crash-landed in the swamps. Fireteam Charlie, led by Staff Sergeant Avery Johnson, followed in their own Pelican soon after. Charlie exited the Pelican into the water of the swamp, with Wallace Jenkins located towards the rear of the formation. Charlie met with Captain Keyes and Second Squad, though the two groups later split up and made their way through the swamp independently. Jenkins and Mendoza were ordered to wait by the facility entrance for the captain to arrive while the rest of Charlie entered the structure.

The captain would eventually arrive, with Second Squad - led by Corporal Lovik - ordered to guard by the entrance. Once inside, Keyes noted that the situation of the facility was entirely different from expected; where they had expected Covenant arms caches and guards was nothing. After exploring for ten minutes, Charlie would stumble across the body of a dead Special Operations Sangheili, as well as many other dead Covenant troops. Unusually, the alien's chest cavity was ripped open in a manner not consistent with human weaponry. When Keyes arrived, Johnson would reaffirm that the dead aliens were not Fireteam Charlie's doing - they had been killed prior to the arrival of the UNSC. Another five minutes of exploring later, and the squad came across a large, locked metal door. Keyes ordered the door opened, despite Kappus' notation that the Covenant had worked "pretty hard" to lock down the door. Nonetheless, Kappus used a spoofer to override the door controls and allow the squad access to a large room.

The team entered the room, and took up defensive positions to cover the captain. Discussion among the troops was interrupted by a transmission from Second Squad - the squad was being attacked by an unknown organism, not Covenant in origin. Johnson ordered Mendoza to head back to their position and investigate, but a door in the room was blown open before the marine could do so. From the opening came a swarm of Flood pod infectors, with the first one managing to strike Private Riley in the back, though the marine was able to grab hold of the creature and keep it at bay while Kappus assisted his friend. More and more Flood forms began pouring into the room, with the marines and captain beginning to fire at the horde. Jenkins, however, was unable to fire due to fear at seeing three or four creatures overwhelm a single human. Keyes was able to catch an infector that attempted to jump at his face, though was ultimately caught anyway by another form that managed to latch onto his shoulder. Jenkins turned to run at the sight of the captain being infected, but was caught by a pod infector in the back.

The now-combat form was fired at by Johnson, but ultimately succeeded in knocking him out of the room. Johnson then proceeded to run away from his now-infected comrades, being fired at by shotguns and assault rifles before managing to escape across an energy bridge, just as the bridge was deactivated by one of the combat forms. Johnson threw some grenades behind him to destroy the pursuers, before finally escaping up the primary elevator out of the facility.

Of the team, only three escaped conversion - Sergeant Johnson, who managed to leave the room in time; an unnamed marine who "played dead", and Mendoza, whose corpse was abandoned by the parasite.

Arrival of John-117
Simultaneously to the raid, Spartan John-117 had been fighting to gain a control of the ringworld's Control Room. Having accessed the facility with Cortana, the AI warned John that Keyes' raid on the weapons cache was a mistake and urged the Spartan to find him before it was too late while she remained in the computer systems of the facility. The Spartan departed the Control Room alone, and was transported to the swamps of the containment facility by Echo 419, landing near Victor 933 ' s crash site.

The Spartan proceeded to progress up the swamp, following the route earlier taken by Fireteam Charlie while being watched by the Flood, whose Marine IFF transponders flickered on and off the Spartan's radar. He found the wreckage of Victor 933 and noted the craft had crashed during takeoff rather than landing, before later finding a similar wreck of a Covenant Spirit dropship. The Spartan would shortly be attacked by the fleeing Spirit dropship Brilliant Gift, who had been infected by the Flood. The Spartan made his way up the swamp, finding only a handful of Kig-Yar and Unggoy and a Shade turret. Encountering the entrance to the Forerunner structure, the Master Chief found some Covenant soldiers running away from human gunfire and several bodies gunned down by plasma fire. Entering the facility, the Spartan found many dead bodies and rooms of gore, but no life to speak of except one Marine survivor armed with an M6D magnum, who attempted to shoot John out of fear. The Spartan took the marine's weapon and attempted to calm him down, but the panick-stricken soldier was too far gone to be of any use.

Upon entering the containment room, John noticed the presence of thousands of empty shell casings on the floor, and Private Wallace A. Jenkins' helmet, which contained a built-in video camera. After seeing the gruesome events of the previous raid attempt through the eyes of Jenkins, the remaining Flood spewed out of nearby doors. The Spartan proceeded to retreat back through the facility, fighting off a tidal wave of flood forms including the now-infected Mendoza, but the Spartan was eventually able to make it out of the facility alive. As the elevator neared the surface, the Spartan once again came back into contact with Echo 419, and several survivors of Second Squad. John-117 proceeded with the remainder of Second Squad, combating infection and combat forms in the open, after being advised by Foe Hammer to take refuge at a tower out in the swamps.

The survivors went through the swamp in search of a tower, which was their designated evac site for Echo 419. After making it to the structure, the Marines were aided by a mysterious ally - floating constructs known as Sentinels. The Sentinels, commanded by the Monitor 343 Guilty Spark, defended the humans, eliminating any Flood in the vicinity - though all of Second Squad ultimately perished. The Monitor then teleported the Master Chief to it, referring to him as "Reclaimer", and then taking him away with him to the Library.

Aftermath
During the initial raid on the facility, almost all of the UNSC and Covenant personnel involved were infected by the Flood. Captain Keyes was later taken to the Truth and Reconciliation to become a part of the growing Proto-Gravemind on the ship, where he was subject to intense mental interrogation by the Flood to mine him of all useful information. He was later finally killed by John-117. The infection form that controlled Wallace Jenkins, through a fluke of luck, was unable to convert the Marine fully, who was now forced to watch as his body was used to fight against his fellow humans in several battles before eventually being captured.

The Covenant Spirit dropship Brilliant Gift left the site and crash-landed in the hangar bay of the Infinite Succor, prompting a special operations group of Sangheili led by Rtas 'Vadumee to board the vessel to eradicate the infestation there.

The results of the Flood outbreak in the facility would lead to the parasite manifesting itself across Installation 04, attacking UNSC forces at Alpha Base and the Covenant in space and around the Truth and Reconciliation. The Sangheili Soha 'Rolamee was tasked with containing the parasite, but was ultimately executed by the Minor Prophet of Stewardship for his failure. Fleetmaster 'Vadamee would later order all ships to undergo an emergency quarantine response and return biometric scans of the crew, or face being fired upon by sterile warships.

UNSC

 * UNSC Navy
 * Captain Jacob Keyes
 * Master Chief Petty Officer John-117
 * Victor 933
 * Unnamed Pelican dropship
 * Echo 419
 * UNSC Marine Corps
 * Second Squad
 * Corporal Lovik
 * Private First Class Chips Dubbo
 * Fire Team Charlie
 * Staff Sergeant Avery Johnson
 * Private Bisenti
 * Private Manuel Mendoza
 * Private Kappus
 * Private Riley
 * "Paranoid Marine"

Covenant

 * Brilliant Gift

Forerunner

 * 343 Guilty Spark

List of appearances

 * Halo: Combat Evolved
 * Halo: The Flood
 * Halo Graphic Novel
 * The Last Voyage of the Infinite Succor
 * Breaking Quarantine
 * Halo: Combat Evolved Anniversary
 * Terminals