6 months after the deaths of Mukozilla, Destoroyah and Godzilla, the amalgamated Earth split back to it's own dimensions once more. The now adult Godzilla Junior stayed behind in his own universe to reclaim the throne as King of the Monsters and carry on his father's legacy. Blossom, heartbroken over Junior's departure, as she felt he was a kindred spirit to her, and having frequent nightmares about his death scene, becomes very reclusive at home, at school, and during her crimefighting activities with Bubbles and Buttercup. Taking notice of this, Professor Utonium, who kept a small chunk of the adolescent Junior's skin, added some Chemical X to it's form, causing it to mutate into a little boy, with many of the same features as the Powerpuff Girls and Rowdyruff Boys, such as a large head, massive eyes, no fingers, and rounded off feet with no toes. However, the boy had spiky, dark red hair and yellow eyes, and had black and white clothes. The Professor was looked on in shock, and walked up to the boy. Initially not knowing what to name it, the Professor gave it the most basic boy name off the top of his head: Tim. The Professor then proceeded to hide the boy, who was seemingly mute. The following morning, Professor Utonium introduced Tim to Blossom, Bubbles, and Buttercup. Buttercup questions why Tim isn't talking, and the Professor replies that he is very shy. The Professor then prepares his 4 children for school. Upon arriving at Pokey Oaks, Ms. Keene introduces Tim to the rest of the class, and the day pushes on. During playtime, a bully comes up to Tim and starts to hassle him. Tim then showcases his own super-strength, throwing the bully across the room and out onto the blacktop. All of a sudden, Tim becomes very violent, and his behavior starts to mirror that of... Godzilla?! Eventually, Buttercup and Tim fight, and the former fights the latter into exhaustion. Later that evening, at home, Tim awakens in his bedroom, and overhears and argument between Blossom and the Professor. Apparently, Blossom managed to put two-and-two together and figured out that Professor Utonium had a piece of Godzilla Junior's skin, and how Tim was the product of combining it with Chemical X. Blossom then yells about how much she hates the Professor and runs up to her room. Tim, in turn, comes out of his room, and begins to ponder if he's really important to this family. He then hides in the kitchen for the rest of the night. The next morning, Tim turns on the news and sees that his "sisters" are getting trampled on by the Rowdyruff Boys. Feeling the sudden urge to fight, Tim showcases another super-power: flight. He then flies to Townsville and witnesses the battle unfold. Looking for a distraction, Tim picks up a rock and throws it at Brick, who, in turn, angrily demands who threw it. Only for Tim to burst out of the crowd and attack him. Tim and brick fight, only for the latter to get knocked through a bunch of skyscrapers. Tim then turns his attention to Butch and Boomer, of whom get mercilessly beaten down. However, the boys then strike at Tim with full force with their eye lasers, only for Tim to unveil his special power: his fiery red atomic breath. Tim's atomic breath cuts through the Rowdyruff Boys' eye lasers like a knife through warm butter, ad sends them into a retreat. Tim then utters out a literal roar of victory, similar to Godzilla's, shocking everyone, including the Powerpuff Girls. Tim then suddenly booms off into the sky and into space. Meanwhile, Mojo Jojo sees this on television at his observatory, and heads into his lab to create a new weapon. The next day, Bubbles heads out to space to search for Tim. She finds him, and convinces him to return home. However, upon arrival, they find that Mojo Joji, HIM, and the Rowdyruff Boys are holding the Mayor hostage. The girls prepare to leave to stop them, but they offer Tim to help them, which Tim accepts. Upon arriving, however, Mojo unleashes the weapon that he had created the night before: Xenilla. Mojo then reveals that he kept some of SpaceGodzilla's skin after the Collision, and combined it with Element X, a counter serum to Chemical X, theoretically making Xenilla a clone of Tim. The girls and Tim fight Xenilla, who easily decimates them due to his telekinetic powers. The villains escape with the Mayor, and the heroes are rushed to the hospital. Tim recovers the fastest due to the regenerative factor in his DNA. However, the Powerpuff Girls take longer, with Blossom taking 2 weeks in the hospital to recover. During this time however, Xenilla betrays Mojo and goes on a destructive rampage, prompting Buttercup, Bubbles, and Tim to go into action to stop him. The trio fights Xenilla, only for the girls to be knocked out of the fight, suddenly, Tim and Xenilla begin to mutate, eventually culmunating with Tim becoming a brand new Godzilla, and Xenilla becoming a brand new Spacegodzilla. They fight, and Townsville is nearly destroyed, until Tim realizes that he is not of this world, and manages to combine his energy with that of Xenilla's and sends the two of them back to the Godzilla universe, with Tim's essence and spirit combining with Godzilla Junior's, and Xenilla's going off into deep space and dispersing.