In FusionFall she appeared, alongside her sisters, in both time periods (now thirteen and in middle school) but was sadly not seen after the heroes escape from Tech Square in the Future, hinting she had fallen alongside Blossom (seen fighting alongside her against Fusion's minions). She's found at City Hall, standing by the Mayor of Townsville, in the Past. She hands out missions to the player, including a mission to deliver a flower to Buttercup during "I'm Still Standing" (a mission Buttercup in the Past can give the player) after hearing she is alive after the battle with Mojo and was surprised she was very close by.
The Bubbles Nano can be acquired by defeating Fusion Bubbles, who is hiding out at the Mount Blackhead Infected Zone. Bubbles' squirrel friend, Bullet, is also in the game and was a victim of Fusion Bubbles' work before the player rescues her and brings her to Numbuh Three to recover (in Bubbles's Nano mission, "Squirrel Squad"). Fusion Bubbles' Secret Lair is at Pokey Oaks Junior High. Fusion Bubbles is also one of three Fusions, the others being Edd and Eddy, whom the player fights three times in the game. She is also one of only two Fusions fought to get two separate Nanos, once to get the Johnny Bravo Nano and once to get her own Nano, the other being Fusion Finn for his own and the Jake Nano. Many of Bubbles' missions involve saving animals in danger, such as birds who have lost their nests in Townsville Park and a beached baby manatee. She also makes her appearance in the battle for Tech Square (The Future) in the Future.
- Octi was the first toy she got from Professor Utonium.
- She once gave Chemical X to an injured squirrel, who later became Bullet, the crime fighting squirrel.
- Like her sisters, Bubbles was designed with more human features, such as ears, a nose and fingers (features she didn't have in the series).
- Fusion Bubbles's backpack is an evil Octi.
- This could be a reference to the episode "Octi Evil" where Him controlled Octi in order to weaken the Powerpuff Girls.
- While most nanos are modeled after the appearance of their respective counterpart in their original show, Bubbles' nano is modeled more after her FusionFall design. This is the same for her sisters Buttercup and Blossom as well.