Set ten years after the original series, the Utonium sisters, now in their mid-teens, have since lost their powers after Ms. Keane was unable to be saved, despite their best efforts. The Mayor is no longer mayor, his assistant Ms. Bellum has left Townsville and joined a government agency, and Mojo Jojo has been put away. The girls have since gone on separate paths. Bubbles is a science geek who seems to be following in her father's footsteps, Buttercup is the only girl on the football team, and Blossom is the quiet girl who moonlights as a ninja-like vigilante, knowing that someday another threat will come to Townsville. But she could never expect how soon.
As the threat looms closer, the new Mayor recruits the girls to save the city with new devices that imitate their powers. As they train, they reconcile their problems, and start to feel bits of their powers coming back. But not everything is as it seems. They soon find that their bond is the only thing that can save the day.