Every episode of The Powerpuff Girls begins with the same introduction sequence, “Sugar, spice, and everything nice. These were the ingredients chosen to create the perfect little girls but Professor Utonium accidentally added an extra ingredient to the concoction -- Chemical X. Thus, the Powerpuff Girls were born using their ultra-super powers. Blossom, Bubbles, and Buttercup have dedicated their lives to fighting crime and the forces of evil.”
Let’s evaluate this sequence. A Professor was in his basement trying to making little girls (a bit creepy but we’ll move on) and he accidentally made these superheroes. While we know Professor Utonium is the man that created the Powerpuff Girls, that's basically all we know about him. Professor Utonium is clearly a brilliant scientist that has the ability to create something as extraordinary as the Powerpuff Girls. Someone this brilliant would have been discovered as a genius a long time ago. It’s shocking that Professor Utonium wasn’t known as a kid genius who had his own laboratory or had his own crazy inventions...
In order to truly understand Professor Utonium we must go back to the very first time we meet the Powerpuff Girls. The first introduction of the Powerpuff Girls is not in the Pilot episode of The Powerpuff Girls, but in fact it is in the cartoon short, Whoopass Stew in the episode titled A Sticky Situation. Whoopass Stew had the same premise as The Powerpuff Girls; it revolved around 3 girls who used their powers to fight crime. It even had a very similar introduction sequence, featuring Professor Utonium.
Now I’m sure you noticed that Professor Utonium looks a lot different in Whoopass Stew than he does in The Powerpuff Girls. Look at him again and you’ll see what’s different about him. His gloves, lab coat and glasses are all different than the later version of Professor Utonium that we know. In fact he resembles another scientific genius, Dexter.
Notice the same gloves, same coat, and even same glasses.
So what does this mean, and why is it relevant to understanding Professor Utonium? Let’s backtrack a little; it is a well-known theory that Samurai Jack and Powerpuff Girls take place in the same universe. There are several billboards and buildings that are present in both the Samurai Jack and the Powerpuff Girls universe.
The premise of Samurai Jack is simple; he is thrown forward through time by his arch nemesis Aku. So we know that time travel exists in this universe and by extension the Powerpuff Girls universe. Look at Samurai Jack and Professor Utonium side by side; they have a very strong likeness. I submit that they are the same person, stay with me on this.
Something had to happen that replaced the original Dexter Professor Utonium with this Samurai Jack look alike. Samurai Jack deals with time travel so it’s not unforeseeable that he would be able to travel to the time when Professor Utonium was creating the Powerpuff Girls. We see in later episodes of Samurai Jack that he has become more dark and ruthless due to his inability to get back to his time. I submit that he managed to get to the point when the Dexter Professor Utonium was creating the Powerpuff Girls and he saw this as a way to fulfill his duty to save others but at the same time, be a part of the happy family that he missed out on. Samurai Jack then killed the Dexter Professor Utonium and created Powerpuff Girls himself using Dexter’s formula. He then stole all of Dexter’s ideas and inventions and became who we now know as Professor Utonium. Doing so created an alternate timeline and the change to Professor Utonium is what turned the Whoopass Stew universe into the Powerpuff Girls universe.