During the Forerunner-Flood war, the Prometheans were converted into artificial intelligences, known as Knights, by the Forerunner machine known as the Composer. These constructs, along with the Didact, survived the activation of the Halo Array, eventually awakening within Requiem and becoming a new threat to the UNSC in 2557.
For thousands of years, the fortified shield world Requiem served as the main command center of the Prometheans. Following the Human-Forerunner war and the discovery of the Flood, the Prometheans, under the leadership of the Didact, stood in opposition to the radical faction of Builders led by Master Builder Faber, who proposed the construction of the Halo Array. They lost the political battle and were subsequently removed from the Ecumene Council, with the Master Builder's allies rising to power in the Council instead. Disgraced, the Didact and some of the other highest-ranking Prometheans were allowed the dignified choice of exile in a Cryptum, while some of the lesser-ranked commanders were accorded more severe punishments.
After a thousand years of exile, the Didact was reawakened amidst the Forerunner-Flood war. Shortly after his revival, a radical shift occurred in the Council, and Faber lost his political power due to his crimes against the Mantle. Called upon to defend the ecumene against the onslaught of the Flood, the new Council elevated the Prometheans back to their former status, and the Didact resumed his duties as the supreme commander of Forerunner military forces.
Under the Didact's leadership, the Prometheans would lead the ecumene's defenses against the Flood until the end of the conflict and the activation of the Halo Array. Near the end of the war, the Didact, still adamant in his opposition of the Halo Array, resorted to the use of the Composer, converting his Promethean warriors, as well as a large number of humans, into powerful robotic forms completely immune to Flood infection. Viewing the Didact's "conscription" of the humans into his army as a severe transgression, the Librarian imprisoned the Didact on Requiem and sealed off the shield world while taking control of the mechanical Promethean forces stationed there, tasking them with preventing outsiders from awakening the Didact.
In July 2557, over four and a half years after the end of the Human-Covenant war, John-117 and Cortana, drifting aboard the wreckage of the UNSC Forward Unto Dawn, came across Requiem. They and a Jul 'Mdama's Covenant force were forcibly pulled into Requiem and crashed on the surface, and were soon after engaged by the Promethean constructs inhabiting the shield world. After John-117 accidentally awoke the Didact, the latter took control of the Prometheans.
Bent on preventing humanity's ascendance to the Mantle in the Forerunners' place, the Didact went to war with humanity, trying to use the Composer to neutralize his ancient enemies forever. The Prometheans and Jul 'Mdama's Covenant aided in this plan, but with the help of the AI Cortana, the Master Chief defeated the Didact and destroyed the Composer and his ship Mantle's Approach with a HAVOK tactical nuclear weapon. However, the Promethean constructs continued to oppose the UNSC forces when UNSC Infinity returned to Requiem in February 2558.