The WAD takes place after the events of The Plutonia Experiment. The failure of the Quantum Accelerator to seal the Gates of Hell and stop a second invasion led to an investigation exposing the UAC's unethical use of gateway technology, putting its surviving officials in prison. The company's assets were divested and transferred to the Union Aerospace Armed Forces (UAAF), a new security force formed to protect our dimension from Hell. To do so, it developed an improved replacement for the Quantum Accelerator called the Hallion Collider. The skeptical press dubbed it "Plutonia 2" in reference to the original incident. While all was well at first, the UAAF was eventually accused by many colonies of abuse of authority, leading the UAAF to be destabilized by guerilla warfare and political games. Doom's protagonist was one of the founding leaders of the UAAF, but was forced to resign thanks to allegations of excessive force while supervising an ex-UAC colony. Nevertheless, having not enjoyed his previous job, he used his freedom to try to solve the conflicts within the UAAF, proposing "Operation Kick-ass" when the situation spiraled out of control. At the same time, however, a study was published finding that frequent use of UAC Berserk packs, Medikits and Stimpacks could cause psychosis and paranoia in those suffering severe trauma. The protagonist's opponents used it to destroy his reputation, ostracizing him from politics. As a result, the internal strife worsened. One day, reports came of Hellspawn invading parts of the Earth once more, with the factions of the UAAF accusing each other of sabotage and espionage or blaming the UAAF itself. The conflict has now devolved into all-out war pitting human versus human, human versus demon, and demon versus demon. Refusing to idle while Hell wreaks havoc on our dimension, the protagonist, armed with only his pistol, tracks down a teleporter to the Amazonian jungle and takes on Hell alone.