More background for Anakin Skywalker is given which ties into later comments in the film, such as Anakin's conversation with a pilot about angels, and Anakin's race in which Sebulba causes him to crash Watto's podracer.
Background for the Sith is given, showing their origin and reasons for wanting revenge against the Jedi.
The first fight between Qui-Gon Jinn and Darth Maul does not end with Qui-Gon simply jumping onto the ship. Maul leaps up there as well until he is knocked off.
Obi-Wan and Maul's duel by the melting pit is greatly extended.