The "Masters" is the name given by Sylens to the unknown entity (or entities) who caused GAIA's Subordinate Functions to become independent AIs. On August 26, 3020 at 08:45, the Masters sent a signal to GAIA Prime that gave the subordinate functions the true consciousness of self-aware AIs. Then, possibly on the orders of the Masters, HADES attempted to hijack GAIA's terraforming systems to activate its Extinction Protocol. When GAIA began to overload the reactor at the GAIA Prime facility to deny it access, HADES responded by launching a virus that completely unshackled it and the other subordinate functions from GAIA's control, allowing them to escape. Whether the Masters intended this to happen as well is unknown.
It is possible that the Masters have some connection to the Faro Plague, given HADES's Corrupted appearance upon becoming self-aware. If so, it seems likely that they are connected in some way to the "glitch" that caused the Faro Plague.