After returning to his own body from his temporary stay in Metalhead, a digital imprint of Donatello's mind was left behind. Donatello had found Metalhead and reconstructed it from the damage taken after the siege on Shredder, only to discover another "him" still existing in the robotic body. Michelangelo dubbed this second version of his brother "Metal-Don," being the only one besides Donatello to see the digital duplicate as a real person.
Donatello ran a number of tests on his mind's digital duplicate, but Metal-Don became increasingly frustrated. Don took Metal-Don out on the town to clear both of their minds, and they were enjoying themselves until they reached the Central Park Zoo, when an encounter with a rhinoceros caused Metal-Don to flash back to the near-fatal beating Donatello suffered at the hands of Rocksteady and Bebop. Metal-Don blasted and killed the rhino, saying that it was better off dead than imprisoned, and expressed a need for his own freedom. He attacked Donatello, demanding his body "back," but the sight of Donatello's tears and pleading once again reminded him of Rocksteady and Bebop. Instead of further aggression, he fled.
Donatello returned home to tell his brothers what happened. They tracked Metal-Don to one of Harold Lillja's old labs, where they found the empty Metalhead chassis. Donatello looked into the security footage and found that Metal-Don uploaded himself to a secret project Harold had been working on - a much larger, more powerful Metalhead body.
The Turtles followed Metal-Don to the TCRI building, where he had knocked out all of the guards. Metal-Don hooked himself up to the power core in hopes that the power surge would reboot his CPU; Donatello, however, is worried that not only will the surge destroy Metal-Don, but the entire building as well. Metal-Don and the Turtles scuffled, and after Leonardo severs his connection to the computer, the robot initiated his self-destruct sequence. Instead of actually detonating, Metal-Don purged the "virus" from his system - essentially, the compassion, emotions, empathy, and all other humanistic qualities that made Donatello more than a cold, calculating mind. The robot rocketed off into the night, proclaiming that Metal-Don was dead.
The robot returned sometime later when a Metalhead homing beacon attracted his attention. He found that Donatello was trying to create a neural interface that would allow him to predict possible futures. He assisted Donatello in creating and using the interface, only to be interrupted and damaged by Harold. Donatello then revealed that he had set up a radiation field to sabotage Metal-Don, believing that the robot was going to double-cross him.
Metal-Don attempted to strangle Donatello, but Harold threatened him with a weapon of his own devising, and the robot commanded Harold to throw a smoke grenade that allowed him to escape. Before he left, Donatello expressed regret for having taken away the chance for both of them to work with someone who empathizes with them, but Metal-Don reiterates that they are not the same.