Knuckles, along with Tails, Amy Rose and Shadow the Hedgehog, was captured by Metal Sonic and Bass. Brought to the extra-dimensional plane of the Skull Egg Zone, the four were roboticized and became the first of Eggman and Wily's team of Roboticized Masters. The four enslaved heroes were then sent to rob the Mega City bank, only to be confronted by Proto Man. Knuckles Man proved more than a match for the heroic Robot Master, knocking away his shield before Mega Man arrived to help him. The Blue Bomber attempted to reason with Knuckles Man and his allies, but the robots attacked him instead. During the course of the fight, a hit from Mega Man's blaster briefly stunned Knuckles Man, but the robot recovered and escaped to the Green Hill Zone with his teammates through a Warp Ring. Once there, they split up in order to rendezvous elsewhere while the pursuing Mega Man was lured away by Metal Sonic. While Tails Man stayed behind to observe, Knuckles Man and his other teammates returned to the Skull Egg Zone with their prize from the bank: the gray Chaos Emerald.
Knuckles Man and his teammates were later sent to engage the de-roboticized Tails and his allies, which included Sonic and Mega Man. After a brief battle, most of the Masters were ordered to pursue the escaping Proto Man while the former Chaotix continued to battle the rest of the heroes. Following the return of this trio to their normal forms, Knuckles Man and Rose Woman remained on the trail while Shadow Man, Silver Man and Blaze Woman were called away for other assignments.
The pair eventually caught up to Proto Man after he had been joined by the restored Chaotix, but were ordered to target Sonic and Mega Man instead and eliminate them by any means necessary. Complying, Knuckles Man and Rose Woman ambushed Sonic's team in a desert region, proving formidable adversaries to the heroes. However, after Rose Woman was restored to normal, Mega Man was able to use her Piko Hammer to overpower Knuckles Man, and a tag team attack by Sonic, Tails and Rush allowed Mega Man to use his modified Mega Buster on Knuckles Man, returning him to his normal form.
Like his organic form, Knuckles Man is possessed of great physical strength, and retains his organic form's knuckle spikes in the form of his "Sharp Knuckle" weapon. However, he is not invulnerable, and Mega Man's Mega Buster has been shown capable of stunning him at least temporarily.
Knuckles Man was dealt a heavy blow by Amy Rose's Piko Hammer and was ultimately restored to flesh and blood by a blast from Mega Man's modified Mega Buster.