In the original timeline, the project was a success and the device was detonated, destroying the planet Minyos. The High Council covered up the incident by claiming Minyos had been destroyed in a civil war. Braxiatel planted a data bomb in the Matrix in order to keep the truth about Project: Alpha accessible in case of an emergency.
In the second timeline, Torvald sent a group of androids back in time to steal the Device. The theft was covered up, since the team that created it did not want to be held responsible for the loss of such a powerful weapon. They told Irving Braxiatel that they had dismantled it. Very few Time Lords knew that the weapon had ever existed; even fewer knew that it was still operable.
However, because the Matrix existed outside of relative time, Braxiatel's data bomb remained even after the timeline was altered. This caused the final timeline when the bomb was detonated by accident, revealing what had happened originally. Romana and Braxiatel went back and stopped the theft, even though it meant that Minyos would be destroyed again. (AUDIO: The Inquiry)