This film was intended to be the show's series finale, but due to the success of the film as well as the show's popularity, SpongeBob SquarePants (1999) was then renewed for a fourth season, continuing the series' run. Further episodes of the series were said to take place before this movie.
This is the last traditionally animated film from Paramount Pictures and Nickelodeon Movies, until its successor, The SpongeBob Movie: Sponge Out of Water (2015), which was released approximately 11 years after the first movie.
The original "cover-up" plot of the film had SpongeBob going to rescue Patrick from a fisherman in Florida. This was an obvious reference to Finding Nemo (2003) and was later revealed by Tom Kenny to be just a "joke" plot which he made up to keep the fans busy.
The ship used for the live action pirate scenes in the beginning was the 1960 replica of the HMS Bounty, a merchant ship used by the British Empire in the late 1700s. The replica ship was sunk in late 2012 by Hurricane Sandy. Interestingly enough, a character in the movie (and series) is named Sandy.
Originally SpongeBob and Patrick left Shell City and met Sandy on dry land and while she gives them advice to take the bus from town to the beach while she's being followed by a group of men in black suits. This scene was cut from the film due to Patrick throwing up repeatedly.