Bubbles first appears coming out of a large model sunken ship after Nemo opens a treasure chest decoration generating bubbles from it, as the yellow tang swims frantically and closes it shut while a nearby starfish named Peach tells Nemo that he likes bubbles, hence his name. He is later seen approaching Nemo hiding in a diving helmet decoration along with Bloat, Deb, and Gurgle, due to Nemo not being comfortable living in the fish tank. When Nemo asks the Tank Gang to know where his father is, Peach tells Nemo that is father might be at the pet store in which Bubbles says he comes from a fish emporium called "Fish-O-Rama". When Nemo tells Gurgle that he is from the ocean, he and Gurgle become surprised about Nemo's answer in which Gurgle calls Jacques to clean him. Later, Bubbles, along with Gurgle, Deb, and Bloat, try to get Nemo out of the tube whom he was trapped into, but a moorish idol named Gill stops them and tells Nemo if he could try escape the tube by himself in which Nemo successfully does so. Later that night, Bubbles and the rest of the Tank Gang accept Nemo into their group while Gill makes a plan to escape from the fish tank.
The next day, Bubbles is seen looking at the treasure chest decoration when Gill tells Nemo a plan how to get to the ocean. After Nemo successfully jams the filter fan by placing a pebble and the filter fan activates again leaving Nemo unable to escape, Bubbles and the rest of the Tank Gang are seen rescuing Nemo before falling into the filter fan. The next day when the Tank Gang makes the tank filthy, Bubbles is seen opening the treasure chest decoration which emits a filthy bubble while Gill tells Nemo and the rest of the Tank Gang that the dentist will clean the tank before Darla arrives to his office. The next day, Bubbles and the rest of the Tank Gang discover that the AquaScum 2003, an upgraded tank filter, was installed into the fish tank, preventing fish from escaping. Bubbles is later seen along with Bloat, Deb, Gurgle, and Jacques helping Gill stop Darla from harming Nemo. Bubbles and the rest of the Tank Gang are seen congratulating Gill for stopping Darla from harming Nemo.
During the epilogue, Bubbles and the rest of the Tank Gang (still in plastic bags) are seen cheering on Peach who successfully makes her way to the ocean. During the credits, Bubbles notices some bubbles that appear at one end of the screen and chases after them.
Bubbles and the rest of the Tank Gang are seen at the post credits of the film, still trapped in their algae-covered plastic bags. He and the rest of the Tank Gang are captured by two Marine Life Institute volunteers upon arriving in Morro Bay.