The Professor finds an old blueprint for an abandoned invention of a dimensional portal (realizing he abandoned the idea as it was unstable). Bubbles peeks above him and tells the sisters about it, which they supplicate him to. A few weeks later, it was finished. The Professor warns the Girls to not use it. However, Bubbles breaks her promise. When the Professor goes to the store, bringing Blossom and Buttercup along, Bubbles stays home and uses it. After turning it on, it sucks her in.
In the 1998 universe of the series, Blossom and Buttercup are re-decorating the house after the party last night. They get interrupted by a crash outside, caused by an unconscious Bubbles from the 2016 universe. Both of the sisters discover it and mistake her as their Bubbles. When she claims that she came from another dimension, they believe that she hit her head after landing, suffering from amnesia. Fortunately, 1998 Bubbles returns from assisting the Mayor. She then notices her 2016 self and exclaims for the Professor. Meanwhile, the Professor and the sisters come home and find Bubbles absent. Hearing a humming sound in the lab, they discover Bubbles has used the dimensional portal. The girls go to the '98 universe to get her back. At Pokey Oaks Kindergarten, '98 Bubbles shows her other self for show-and-tell. After school, Bubbles befriends her '98 self, though she tells her that her voice is annoying to her response.
Meanwhile back in the 2016 universe, Silico had discovered the Professor's portal from hacking into one of the severance cameras in the lab, giving him an epiphany; to destroy the Powerpuff Girls by creating a device to wipe out any dimension from existence. With the 2016 Girls and Professor, they have entered the 1998 universe and find Bubbles. In a montage, Bubbles is guided by the 1998 Powerpuff Girls around their Townsville. Bubbles, the Girls and Professor go shopping at the Malph's grocery store, where the 2016 counterparts find her. Before they bring her back home, Bubbles introduces their 1998 counterparts and persuades her Professor to stay for the night, in which he allows. Back at the Utonium residence, the Professors engage a conversation on their differences of their respective dimension. The Girls explain their previous adventures to their 2016 counterparts, which interest Blossom and Buttercup in excepting their 1998 selves.
The next day, the hotline rings and the 2016 Powerpuffs answer it and get informed that Princess Morbucks has robbed the Bobbin Brothers Jewelry Store (which confuses them as their Morbucks has never done that before). The Girls stop her in time, much to the 1998 Girls' dismay, leading to Buttercup calling out the three for their absurd personalities and differences. Called back at the lab, the Professors show them a message from Silico, which informs his plan on destroying the 2016 dimension, followed by the 1998 one. He had already wiped out the three other dimensions to prevent them from getting assistance from their other counterparts. 2016 Professor explains that if Silico wipes out his and their dimension, every inhabitant, even when outside their dimension, will fade from existence. After explaining, he starts to fade away, as an indication that the 2016 dimension is in the process of being wiped out.
Meanwhile, Silico, operating a robotic mech, has arrived in the 1998 dimension and teamed up with its villains to keep the Girls from stopping his scheme. The Girls, realizing that they will be next to fade from existence, head out to find Silico with their 1998 counterparts by their side. They encounter their counterparts' villains who prevent the Girls from stopping Silico. The 1998 Girls fight and hold off their enemies while their 2016 selves head to Silico's mech found downtown. The Girls infiltrate the mech and find a monitor screen inside, with a chart that shows the progress of the remaining and destroyed dimensions. Silico traps the Girls in a glass cage, as he had figured they would come if his cronies would fail to stop them. He turns a monitor that shows the progress of their dimension being erased.
The 1998 counterparts arrive, but not stop him, as they explain that he, too, will be erased from existence, which happens now, much to Silico's dismay and regret. After fading completely, they rescue their 2016 counterparts and they stop the machine with Bubbles hacking into the computer, shutting down the process before the 1998 dimension was next. Unfortunately, the 2016 dimension has hit "100%", leading to the Girls to fade from existence, with Bubbles being the last one remaining for a few seconds, wishing they would have been more like their 1998 selves. The 1998 counterparts hug her, then she fades away completely. After she does, Silico's mech disappears around them as well. They then spot their enemies, awakening from unconsciousness. The Girls decide to fight their villains as dedication to their death. The Narrator concludes the story by saying "So once again, and for the last time, the day is saved, thanks to the Powerpuff Girls! You know the ones I'm talking about."