In the film, SpongeBob and Plankton travel through time, with SpongeBob claiming them to be lost in time, and somehow end up at an unknown location in Bubbles' Inter-Dimensional Spacecraft and encountered Bubbles. At first glance, he is watching Saturn and Jupiter, leaving his face unseen. When the duo ask who he is, he says that they call him 'The One Who Watches.' When they ask if that's his real name, he turns around to show that he is really a dolphin named Bubbles, with Plankton claiming it to be a dumb name. Bubbles then explain that for the last 10,000 years, he was watching the Earth to protect it from various disasters. He took the opportunity of their presence to take a few minutes to go to the restroom and told SpongeBob and Plankton to keep an eye on things and never touch anything. SpongeBob tells Plankton to look at the one with the eye and that he will look at the ringed one as a way of teamwork. They soon see that Jupiter and Saturn are getting closer to each other. Plankton wonders if it's supposed to happen and if they should get Bubbles, with SpongeBob saying it will be fine. The gas giants then collide with each other as chunks of both planets make their way through the triangular 'window.' SpongeBob tries to hide the rubble under the floor like dust under a carpet, only for it to cause a huge lump on the floor. After Bubbles got out of the restroom, he tells SpongeBob and Plankton that they are free to go, until he notices the collision of the two gas giants just as Saturn's rings fall off. He argues that he will be fired from his position and then turns his attention to SpongeBob and Plankton, telling them that he will end their lives. He then attempts to kill them by firing red lasers out of his blowhole until the two troublemakers make it back to the time machine.
Sometime later, Bubbles encounters SpongeBob and the gang nearing the surface via through a triangular portal. SpongeBob screams Bubbles' name in fear as Squidward asks if he knows that guy. SpongeBob then apologizes and pleads Bubbles to not hurt him or his friends. Bubbles then explains that he wanted to get out of his dead-end nowhere job, saying he didn't have the courage to do it himself. And as a reward, he helps them get to the surface and tells the group to jump into his mouth. Squidward and Mr. Krabs then argue about the idea claiming he just wants a snack. As an argument occurs, Bubbles quickly scoops the gang into his mouth and proceeds to the surface. Bubbles then jumps out of the ocean while doing front flips and opens his blowhole like an airlock as 'pixie-dust'-like particles sprinkle onto SpongeBob and friends, giving them the ability to breathe above water. Bubbles launched SpongeBob and his friends out of the blowhole and they landed on the beach. Bubbles then leaves saying there's nothing more he can do and that the rest is up to them.
Bubbles is later mentioned by SpongeBob to Burger-Beard the Pirate telling him how he and the gang were able to breathe on the surface. Burger-Beard responds to this by saying there's no dolphin in the book.
Before the credits roll, when Burger-Beard the Pirate helps the seagulls sing the theme song, Bubbles tells them to keep it down and soon has a rap battle with one of the talking seagulls. The seagulls win and Bubbles rewinds the time so they could finish their song. At the end, he actually starts to show appreciation to the song, which might be a portrayal of adults' attitudes towards the show.
Role in the series
Though being fired as a galactic guardian, Bubbles still serves as a godly guardian figure, including being a time lord like Saldaron, as well as a space lord, who watches over spatial fabric just as much as time. He has helped aid in more than SpongeBob's 2015 Krabby Patty crisis, as during the events of The Truth of the Legends of Bikini Bottom he helped them stop Drainthus for his plans with the Main Drain, which was different than what was portrayed as reality was manipulated to the episode's events until Bubbles reversed it back, and admits to being capable of warping more than reality, including continuity, being able to be friends with SpongeBob during the days before 2015 on the day before the Main Drain Episode, to help guide them into stopping Drainthus with Commodore Nemo.