Sidious/Palpatine was "the phantom menace," that much was clear long ago. Palpatine takes advantage of a major crisis and maneuvers to get elected Supreme Chancellor....Maul (the Sith apprentice) is defeated and believed dead....and as Yoda and Mace discuss which Sith was actually the Master there's a partial camera zoom on the profile of Palpatine as he sternly watches Qui-Gon's funeral pyre.
Palpatine was behind the events in Episode I (of course it didn't hurt that the voice, lower face and chin of Darth Sidious were identical to Palpatine's
). Plus, if you collected Star Wars figures before 1999 you knew that the Emperor's name was Palpatine. So....there's that.