Bubbles moved along with her sisters to Megaville and attended the Megaville Elementary. Their introduction didn't went as planned however, as they weren't believed to be heroes. Dexter however did take them serious and later challenged Buttercup to a duel. Dexter proved however to be stronger than he looked and Blossom decided to interfere in their duel. After helping Buttercup, she called Bubbles to assist them in the battle. Surprised but joyous, she joined the battle. The battle was broken prematurally by Jack however, who withheld from taken disciplinary actions, since it was their first day. Instead, he invited them to his dojo, where assigned Dexter as their guide for the school.
In his dojo, Bubbles was distracted by Jack's dog, Courage, expressing her love for animals as she showed him to her sisters. Jack told them how he got Courage and decided that Courage deserved a new owner, Bubbles. She took him outside where she played with him, until she got attacked by the Dread Dragon. Courage called for help and the girls were drawn into battling the monster. At first, they were outmatched by the creature, until Jack appeared, who slew the monster eventually. The next day, Bubbles, trying to make friends, "befriended" Mandy, being completely oblivious of the latter's dark nature.
Some time later, she was hugged by Blossom, after the latter witnessed Dexter's tragic backstory, leaving both Bubbles and Buttercup wondering what got into Blossom. After Blossom was kidnapped by Mandark, they were talked up to speed by Otto Osworth and together with Buttercup, went on a rescue mission to save Coop, Dexter and Blossom. Narrowly, they escaped Mandark's lair-turned-deathtrap and returned home.
Months after the events of Mandark's Revenge Arc, Dexter accidentally released a Globmonster, a creature that he couldn't beat with his tech and ended up absorbing him. He was however saved by the Powerpuff Girls, as Blossom froze the monster, Buttercup threw it in the air and Bubbles broke it to pieces, before returning to school. At school, it is revealed that she has befriended Mandy and Gaz. It was then that she saw Olga for the first time. Mandy explained to her that Olg led the Megaville Elementary Dance Troupe, sparking Bubbles interest. She immediately signed up for the try-outs and shortly after, trying to convince Blossom and Buttercup to come along. While Buttercup outrights refuse to come, Blossom tried to make up an excuse, which fell on dead ears as Bubbles took her to the try-outs. After Dexter solved some technical difficulties, Bubbles did a succesful try-out and was selected for the troupe. After learning that Dexter and Blossom have some problems, Bubbles came up with the idea to go the beach with some friends. A change of environment might help them to talk things out. Back at school, Bubbles met Gaz' brother, Dib who chased by Gaz for batteries and later Jenny. Bubbles appeared to idolize Jenny and was ecstatic to learn that their parents were colleagues.
During the performance at the science fair she was about to dance when suddenly GIR intruded. Jenny tried to stop him but GIR put a controlling device on her forehead, transforming Jenny into a portal between the Cluster Zone and Megaville. The invasion began and the girls were battling the Cluster crowd. Bubbles tried to save Olga from one of the Darkstar Councils but got hit by Bell and was knocked out. Bubbles went further with evacuating the people on the science fair. Bubbles and Courage were having a hard time trying to get the door to the safe room to open, since the scientists said they needed someone with a serious amount of muscle and Bubbles was the only one left that has super strength that can do it. When Courage kicked the door and injured his foot, Bubbles quickly kicked the door herself and knocked it down, as "punishment" for injuring Courage's foot. Bubbles looked inside the safe room and saw all of The Central Megaville Skyway Hangar's equipment that the Professor kept in storage, even Dynamo. Bubbles was telling the people to get inside the safe room and Olga wanted to ask Bubbles a favor, but Bubbles was thinking too much about Dexter to respond to Olga's hand in need. Bubbles started to pay attention and started screaming out to Olga. Olga wanted her to go and get Dexter, but Dexter came to her first and told her that they have a serious problem that needs to be taken care of. Bubbles was told by Dexter that he can't keep fighting off the monster and that they need to get the safe room door closed now. Bubbles was having trouble closing the door after she kicked it open, but then the Professor helped her by activating Dynamo. The Cluster monster tried to get in by infecting Dynamo with a virus, which led the Professor to shut her down for a cold boot-up. Bubbles is now the only one responsible for keeping the door closed from the Cluster monster. She was seen using her laser eyes to keep Cluster monster away with Courage. Later, although they were relieved that the Cluster monster fled in fear of the explosion, she became very sad when not only she and the others were going to be demolished by the explosion, but also because her sisters had failed to diffuse the bomb and might have died.
After she realized that she and the others were still alive, she expressed her belief that Blossom and Buttercup will fine as well. When she heard Jenny's scream, she flew in the stage, in order to save Jenny. Her sisters were all ready on the stage, shocked to see that the Rowdyruff Boys have returned. Bubbles seemingly ignored this as she ran towards Jenny, claiming that she needed their help. At no point does Bubbles seem to care about the presence of the boy, while she tried to help Jenny. Together with Courage, she tried to reboot Jenny and was later helped by Noreen Wakeman. Suddenly, she was confronted by Boomer. Creeped out by his strange behavior, she tried to ask him what he want but instead he surprised everyone in the room by kissing her on cheek. As Brick tried to uncover his brother's plan, he recalled that when they were kissed, they exploded. This mere suggestion was enough to freak out Bubbles, before Blossom restated that she wasn't unstable, at least not physically.