The player takes on the role of the Director General of the "Department of Agriculture and Fisheries", a non-existent Executive Agency that conceals a secret police which keeps the government popular by any means necessary. Answering only to the Prime Minister, the Director General has the power to use wiretapping, surveillance, smear tactics, disinformation, burglary, kidnapping, torture, and assassination to keep the government popular with the people.
In addition to the Director General's regular duties suppressing and removing those who threaten the status quo, there is also a subplot involving his membership in a secret society called "The Secret Masters of Thoth". These missions, which are received from a "Secret Master" wearing the vestments of an Egyptian pharaoh, involve more bizarre opposition than regular missions; these missions include protecting a fellow member from a Mafia assassination, foiling an attempt to subvert the nation by pod people in key positions, the protection of the Church of the SubGenius from a scandal, and restraining the growing power of the Illuminati, among others.
Source: Wikipedia, "Floor 13 (computer game)", available under the CC-BY-SA License.