The Second Ark Conflict was a battle between the UNSC forces aboard the Spirit of Fire and the Banished forces under command of Atriox on Installation 00 in 2559. The fighting began when the Spirit of Fire, which had been adrift in space since the events of the Battle of the Etran Harborage, arrived at Installation 00 and came into contact with Banished forces. The Banished had arrived at the Ark on November 25th 2558, a month after the portal to the Ark was closed because of the Created uprising, and immediately destroyed the UNSC research outpost on the surface.
During the conflict, Spartan-II Jerome-092 was able to infiltrate the Banished's CAS-class assault carrier Enduring Conviction and use AI Isabel to fire the ship's glassing beam onto the surface of the Ark, activating the Installation defenses. This response resulted in the destruction of the carrier.
Meanwhile Professor Ellen Anders was able to initiate the deployment sequence for the new replacement for Alpha Halo, Installation 09. Attempts were successful in disabling the ring's firing mechanism, but she was unable to stop it before it left the ark towards the Soell system with her on-board.
The battle continued between the Spirit of Fire and the Banished, and in June, Banished forces accidentally released the Flood from containment around the wreckage of High Charity, which had been infested with Flood and crashed on the Ark during the Battle of Installation 00 in 2552. The Flood outbreak was contained, though at a high cost to the Banished forces.