Intro: Open with Leonardo entering a small Medieval tavern full of little elves. Once Leo's inside, the angered elves draw short swords and close in on the Turtle. Leo leaps into action and gains the upper hand in the battle, but one of the little buggers blows on a horn and a huge rock troll stalks into the bar. Cody and Master Splinter appear and Jones worries about Leo's safety - Master Splinter tells the boy to watch and learn. Leonardo dodges attacks from the powerful monster and then cuts a chain, causing a huge chandelier to fall onto the troll, smashing it into the floor. Having conquered all opponents, the scene flickers into Leo’s true surrounding where we see that he's actually in the middle of a holographic simulation room, standing over a defeated battle Bot. This was the initial test of Cody's new invention - a holographic Turtle Dojo. Satisfied with the results, the trio heads out to retrieve Mike, Don and Raph. As the group exits, we see the Bot flash with residual energy as its circuits ominously crackle.
Act 1: Donatello is working on the kitchen bot in Cody's penthouse apartment, trying to make adjustments so it will prepare their food better. Things go haywire and Serling is caught in a fiery blast - fortunately the robot is unharmed. Raphael grows impatient with all the noise and stomps off to find some privacy - on his way he's intercepted by a cleaning bot that attempts to brush his hair, give him a shave, sprays him in the face with water and forcibly brushes his teeth. Needless to say, Raphael isn't too enthused by the future.
In a nearby city power substation we see two technicians view their computers in alarm - a massive power surge threatens to overload the entire system. Sparks begin to shoot out the control panel and a giant surge whirls up and begins running through the power lines. Red energy coalesces into a sharp face that shrieks with joy now that it's free. The energy creature then uses power lines to escape the power station. The confused technicians note that the danger seems to have passed and decide to go to lunch.
Cut back to the penthouse where Cody shows the other Turtles the new dojo that he built for them. It's a high tech training facility with battle simulations and over 500 holographic background modes. As Cody cycles through various environments, Raphael is still in a bitter mood an is unimpressed. After some prompting from Master Splinter, Raph begrudgingly thanks Jones. Splinter then announces that as a measure of their gratitude, Leonardo will begin instructing Jones in ninjitsu. Cody leaps into the air with joy, expecting to learn combat moves. Leo tells the boy to sit down in lotus position, as their first lesson will be to meditate on the importance of the mind/body connection. Cody is disappointed by this development, but he tries to meditate. Just then, the power surge hits their building, causing an alarming flux in the energy powering the dojo. Don and Cody exit to investigate. Suddenly the doors slam shut, trapping Splinter, Leo, Mike and Raph inside! Back inside the dojo, the strange red energy appears and once again the maniacal face appears and announces that it is in control of the building - and it will use its prisoners in the dojo to get what it wants! With that, the energy being uses the dojo's abilities to launch attacks on the TMNT. Master Splinter is hit by an electric prod that weakens him. Leo rushes to his Sensei's side - fortunately the old rat isn't seriously injured, but he won't be able to continue fighting.
Act 2: Meanwhile, Don and Cody have logged onto the building's security system and have discovered that a massive program is traveling through the computer array. Remarkably, there's nothing that they can do to shut down the rogue program or delete it. Serling interjects and connects himself to the system in effort to help, but he's immediately engulfed in the red energy that's been plaguing the city. The servant bot loses control of himself and begins attacking Don and Cody with a mop! Serling is able to communicate, but he cannot control his actions.
Don and Cody escape from Serling and race to the dojo to get help - only to discover that the others are locked inside and facing a menace of their own. Serling arrives and once again the red energy erupts into the air and the evil face appears. The entity introduces itself as Viral and explains that she wants to get into O’Neil Tech’s mainframe to steal the technology located therein - but to do so, she needs Cody’s passkey. Jones scoffs at the idea that he would give up this information, and Viral threatens that she will destroy Splinter and the others inside the dojo if she doesn't get the password.
Meanwhile, inside the dojo, Splinter and the Turtles find themselves standing in an old west saloon simulation where they're attacked by the Wild West C.O.W.Boys of Moo Mesa. Outside, Don and Cody once again flee from the possessed Serling. Viral chases them and eventually Don and Cody crash through a window!
Act 3: The villain thinks that the duo have fallen to their deaths and heads back to the dojo. Outside, Donatello has managed to puncture the building's exterior wall with his energy bo. Fortunately he and Cody are right next to an air duct, so Don kicks it open and the two reenter the facility. Once safely inside, Donatello comes up with a plan. The brainy ninja points out that Viral can only hack into computers via hardwire connection, not by wireless. So, if they shut down the power grid that the building is on, they’ll isolate Viral in the building. Once that’s done, they can simply shut down the building's power and purge her from the entire system.
Cut back to the dojo. Viral arrives expecting to find dead Turtles, but instead discovers that they've made friends with the C.O.W.Boys! Enraged, Viral attacks.
Elsewhere, Donatello puts his plan into action, and for five blocks around the building, power systematically shuts down. With Viral isolated in Cody's penthouse, Don quickly shuts down power in the building. Inside the Turtle Dojo, the holographic enemy crackles with energy, floats into the air, and then disappears!
The dojo doors finally open. Cody and Don come inside to explain what they did, but just as it seems to be over, Viral tears through a wall and enters the room! The villain has taken over the Dojo Battle Bot's body and is angrier than ever!
Act 4: As Viral attacks, the Turtles gang up on her - pleased that she is now in a physical body that can take real damage. With nowhere else to upload to, Viral cannot escape the ninja onslaught. A very damaged Viral makes a run for the elevator, but the Turtles catch her and kick her down the deep elevator shaft.
Later, the Turtles and Jones arrive in the trashed penthouse apartment. Serling is back to his old self and worried about cleaning up the mess. Raph reports that Viral survived the fall and has escaped. We also discover that Splinter has regained his strength. The Sensei points out to Cody how Donatello displayed the importance of mind while his brothers proved the value of body in their battle. Jones states the he understands the importance of his first lesson and he and the others begin to meditate. Raph wanders off to read in peace but is dismayed when he sits in a robotic chair that begins speaking to him.
Cut to a utilities access tunnel where the damaged Viral is kneeling. A shadowy figure enters and Viral begs for repair. Viral's master is Sh’Okanabo, the mastermind behind the plot to take over O’Neil Tech and retrieve its secrets. The evil overlord tells his underling that she will stay in this body as punishment for her failure. While this attempt did not reap results, it's obvious that Sh'Okanabo won't be giving up any time soon...