Donatello has dragged Michaelangelo to a scientific convention so that Don can hear the mutant-related theories of the eccentric Dr. Quease (Donny thinks the Doc is brilliant, Mikey thinks that he's a quack). Quease, ever on the edge of scientific discovery, wears a direct nueral (brain) implant that jacks him directly into the internet, as well as giving him the ability to jack into any computerized machine.
Suddenly, a group of the Dragon Lord's Rank warriors burst into the lecture hall and abduct Dr. Quease, escaping before the TMNT have a chance to react.
The Dragon Lord has captured Dr. Quease in order to combine the doctor's scientific expertise with DL's vast occult knowledge. The Dragon Lord attempts to entice Dr. Quease to work for him by giving him a lab full of state-of-the-art equipment. Amongst the apparatus in this lab is a stolen classified device called the Heliumcooled Cyber 600, the most powerful dissection machine ever built, and something that Quease had only dreamed of working with.
Donatello, meanwhile, tries to convince the other Turtles to mount a rescue attempt of the Doc, but the others think that it's too dangerous to risk a break-in into the Dragon Lord's HQ. And so, under cover of the night, Donatello sets out to rescue Dr. Quease... alone...
After successfully sneaking into Dragon-central and freeing Quease, Don gets captured by the Dragon Lord's forces due to the "good" Doctor's suddenly agreeing to side with the Dragons. Now, with the capture of Donatello, the obviously mad scientist has a perfect mutant specimen... to dissect!
Fortunately for Donny, the other Turtles come to his rescue. While Leo, Raph and Venus battle the Rank Dragons in a whirling wonderment of Ninja and Shinobi-style martial arts mayhem, Mikey successfully frees Don by splicing Quease's nueral brain jack directly into one of Mike's hand-held video games, which sets the quack scientist fighting against the Dragons like a remote control toy!
Vanishing into the sewers, Don admits to his fellow Turtles that he was wrong about Quease... the Doc wasn't a brilliant scientist but a mad one! Donny admits that he was blinded by his love of science.