It is Career Day at Pokey Oaks, and the Professor shows to the class a time machine and explains how he got into science and created the Powerpuff Girls. But Mojo Jojo overhears everything and uses the machine to go back in time to that specific time period in order to prevent him from getting into science at all costs. But the Powerpuff Girls also go back in time and are hot on Mojo's trail.

"Nano of the North" It's raining in Townsville, but this is more than just rain. These drops are really microscopic robots tearing apart the city and the Girls must fight with these creatures on their own level.