In filmmaking, scenes are often cut, shortened, or unrealized prior to the film's release. Nickelodeon movies are no exception, with many scenes written and even filmed but dropped from the final edit of the film.
- Right after the scene with the circus commercial, Stu and Didi have a nightmare where Dr. Lipschitz lectures them about their parenting. This scene was reinserted into the movie in its televised broadcasts on CBS and Nickelodeon, and the part with Stu and Didi looking in the book right before the nightmare was incorporated into the novelization (the actual nightmare was left out). However, it is not included on the video releases. A sketch of Tommy and Dil tugging on the Stu and Didi puppets in the nightmare can be seen in the Rugrats: Still Babies After All These Years documentary.
- After Angelica and Spike get lost in the forest, there was a brief scene where the Rugrats are pulling the Reptar Wagon up a hill, all the while singing an army chant. Chuckie and the twins sing that they want to get rid of Dil, but Tommy doesn't want to. This scene was included in the novelization and was also reinserted into the movie's televised broadcasts on CBS and Nickelodeon, but is not included on the video releases.
- The DVD includes two short scenes, likely meant to be used immediately after the end credits, in which it is shown what happened to Coco and Jean-Claude after the movie's events. In the first one, it is shown that they're now loading passengers on the Ooey Gooey World, while in the second one, they're working at a perfume factory, testing underarm deodorant and foot powders. It is unknown why neither of these two scenes were used as a post-credits scene in the actual film.
- In the theatrical trailer, there is a brief shot where Cindy is shown telling Jimmy, "If we blow up, whatever's left of me is kicking your butt." Television commercials for the movie had the line changed to "If we crash, whatever's left of me is kicking your can." In the print novelization, Cindy says this line right before the kids blast off into space.
- The trailer and novelization also include two other lines of dialogue from Cindy that were ultimately unused in the film. The first of these is her response to Jimmy introducing his Shrink Ray, which was originally "Will it work on your big head?" (in the finished film, she says "What's the matter, Neutron? Aren't you short enough already?") The other line is "For a nerd, he sure comes in handy." The trailer suggests that she was to say this right before she and Jimmy smile at each other while flying through space. The novelization, however, has her saying it to Jimmy after he saves her from being attacked by one of the Yokian guards.
- The novelization also includes a few other scenes that were cut or changed in the movie itself:
- A prologue scene is added, showing the Yokians arriving in the solar system and setting a course for Earth.
- The scene with Cindy and Libby in Cindy's room (right after Jimmy sneaks out of his house) is slightly longer. Libby asks Cindy if she ever thinks about getting married. Cindy balks at the idea, because she thinks boys are disgusting, but Libby teases her about her crush on Nick.
- Another scene with the Yokians arriving on Earth while Jimmy, Carl, and Sheen are at Retroland is included. The Yokians on the ship receive a video call from King Goobot, and when one of the crew members fails to salute, he is promptly ejected into space. Goobot proclaims to commence kidnapping the humans, reminding Captain Spoor (see below) to only grab the large specimens because "size does matter."
- After the sequence with the kids celebrating not having their parents around, there is a scene where the Yokian ships return to Yolkus with the enslaved parents. King Goobot tries out the remote control for the Hats of Obedience, using Hugh Neutron as his test subject. But then Hugh's Hat malfunctions and he briefly reverts back to normal, much to Goobot's annoyance. When Captain Spoor's first officer points out that it was a result of the device being manipulated too aggressively, Goobot obliterates the unfortunate Yokian with his Doomstick (a device not seen in the movie).
- After the kids blast off into space, there is an extra scene with King Goobot and Ooblar at the Yokian marination plant, discussing their plans to feed the adults to Poultra. They then start poking each of the adults, making them yell out in pain.
- After Jimmy shuts off the hypnosis on the adults and they begin to escape, King Goobot uses his Doomstick on Ooblar.
- During the kids' battle with Poultra, there's a brief scene where Sheen sneaks around the spaceport hangar and hijacks the large space freighter that the humans later use to escape Yolkus.
- The novelization includes a Yokian character called Captain Spoor, who is in charge of their expedition to the solar system and, in the novelization, is the one who receives Jimmy's message. A brief clip and audio of Spoor (voiced by Kevin Michael Richardson) watching Jimmy's message can be seen in the theatrical trailer. In the finished film, that scene is changed so that King Goobot directly sees the message himself.
- The film was originally a 90-minute special, but the test screenings were so positive that Paramount decided to remake it as an 80-minute film released in theaters. One notable cut was the character Tiki, a little animal whom Eliza communicated with and who accompanied her, Darwin, Spike and the babies, who were actually going to interact with Eliza throughout the course of the movie. He was voiced by rapper and actor LL Cool J; all of his scenes were cut from the final film, for some reason.
- Four deleted scene that happen watch 3 songs and a conversation of Betty and Didi.
- One deleted scene shows SpongeBob and Patrick meeting Sandy (depicted as a live-action squirrel) on land. In this deleted scene, Shell City is an actual city where Sandy constantly gets pursued by squirrel exterminators in black suits. She also mentions that there are buses that arrive here and Bikini Bottom.
- During SpongeBob's awakening in the Goofy Goober Party Boat, he asks for a "double fudge spinny." This line was rejected from the film, but was still used in the Ice Cream Dreams book which is loosely based on the movie.
- There is also a deleted scene where Mr. Krabs appears in SpongeBob's room. This was cut to save time.
- There is a full version of "Down on the Farm", which was animated, but not included in the final film. The full version is included on the soundtrack, however and an extended version is in the video game.
- During the montage, there is a sequence of Otis, Pip, Pig, Freddy and Peck relaxing on a hill and Pig gets a bottle stuck in his crack. This was later used as a promo for the series.
- Freddy has a conference with Dr. Filly, who would later appear in an episode of the series. This actually was made
- There is a song called "Barnyard Bop", in which Hanna sings a ballad about Otis for the opening. This was fully animated, but cut out from the final cut. Later on in the film, Otis sadly walks back to Ben's hill after failing to run off the coyotes and Hanna sings a sad reprise.
- After that, Otis runs into his friends, who think he ran off the coyotes and start cheering for him. This makes Otis more irritated and he runs away. After that, he has a conversation with Miles, who tries to give him some pep talk.
- The trailers and commercials showed a gag from the climatic battle that does not appear in the film itself, in which Burgerbeard throws a plastic six-pack ring at Squidward. The six-pack ring gets caught on Squidward's nose, and his attempts to get it unstuck only make it worse.
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