While Mecha Sonic and Bunnie Rabbot were locked in battle, Tails recruited Knuckles to stop Mecha Sonic. Knuckles was heavily injured previously from trying to stop Mecha Sonic, forcing Princess Sally to carry out "Operation: Last Resort." They used a portable Roboticizer (the same one that partially roboticized Bunnie), to roboticize Knuckles, and used a Neuro-Overrider that would allow Knuckles to retain his free will. As Mecha Knuckles, the two were evenly matched, until Mecha Sonic hit Mecha Knuckles with enough force to set him on a collision course with Robotropolis, and a hefty supply of nuclear warheads. Knuckles used his magnetic claws to take Mecha Sonic down with him, and both barely survived. Mecha Sonic was practically inoperative, but Mecha Knuckles was intact enough to knock out Robotnik (who had retreated to his nuke-proof shelter), and fly Mecha Sonic back to Knothole. Mecha Knuckles was de-roboticized easily, and with minimal injury.
His only other appearance as Mecha Knuckles came unexpectedly when Knuckles, as Chaos Knuckles, attempted to restore the Floating Island by altering history. His third and last attempt, preventing the death of his ancestor Edmund, caused Knuckles to somehow become Mecha Knuckles again. When it looked like the change was irreversible, Knuckles instinctively undid his blunder. As Edmund's brother Dimitri explained to Knuckles and Julie-Su, had that Dark Legionnaire not assassinated Edmund, there would have been no need for the creation of the Brotherhood of Guardians, leaving the Floating Island vulnerable to Robotnik's conquest.
Powers and abilities
Like Knuckles, Mecha Knuckles has a great deal of strength, and is capable of flight. (As this was before Knuckles learned of the Chaos Force, it is unknown as to how his link to Power Chaos was affected.) His greatest feature, however, is his magnetic "Knucklaws." They are not only able to completely block two full laser blasts, but using the claws in that manner drains the opponent's batteries. Additionally, they can generate a strong magnetic field that even Mecha Sonic could not escape from. To add insult to injury, since one of Robotnik's older roboticizer units was used, that meant significantly fewer "foreign inferior parts" were used, which Mecha Knuckles used as part of the reason as to why he had less damage from the nuclear blast than Mecha Sonic.