Numerous theories have persisted in claiming deeper significance to the Watergate scandal than that commonly acknowledged by media and historians. In the book The Ends of Power, President Richard Nixon's chief of staff Haldeman claimed that the term 'Bay of Pigs' was used by Nixon as a coded reference to the Kennedy Assassination in a White House conversation recorded on the Watergate tapes. This same theory was later referred to in the Oliver Stone Nixon biopic.

An alternate theory to the mainstream media account of the Watergate scandal can be found in Silent Coup, a 1991 book by Len Colodny and Robert Gettlin. The two authors believe that it was Nixon's silent war with the Pentagon that ultimately led to his removal from office. The book was widely criticized for leaps of logic and weak evidence, and its theories enjoy little support from either professional historians or the general public.

Another theory to the resignation of Nixon is that he was secretly promised a pardon by Ford. In order to save his own skin, Nixon resigned from Presidency in return for a pardon.