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Mecha Sonic achieves this Super Form by jumping on top of the Master Emerald and absorbing energy from the Emerald directly into a red power core in his chest. This transformation turns Mecha Sonic a golden-orange color, and makes him invulnerable to attack. He also gains the ability to hover at the top of the screen for extended periods of time. However, he is unable to sustain his power for very long and will soon revert to normal form and attempt to recharge.
In this form, Mecha Sonic attacks by spinning toward Knuckles' current position, firing three charged balls of energy. This seems to be the attack that drains his energy, although other attacks include trying to ram into Knuckles at full speed and using a spindash attack that aims at wherever Knuckles is standing. He can only be damaged while powered down. Halfway through the battle however, the attack pattern completely changes and Mecha Sonic hovers back and forth at the top of the screen, stopping to fire a series of thick damaging rings. He occasionally loses power for a split second, for unknown reasons, causing him to momentarily drop. This is Knuckles' chance to attack, but he doesn't even touch the ground so the player only has a few seconds before he powers up again.
If Knuckles has collected all of the Chaos Emeralds (and, if playing Sonic the Hedgehog 3 & Knuckles, all of the Super Emeralds), then Mecha Sonic's Super State is completely destroyed at the end of the boss battle. However, if the Emeralds have not all been collected, Mecha Sonic reappears at the end of the credits, sparking with glowing red eyes while standing on top of the Master Emerald.
Because this boss was only ever intended to be fought by Knuckles, if the player uses Debug mode and uses Sonic to fight him, the ending will glitch and a blue Knuckles will appear riding on the Tornado.
If the player finishes this fight as Tails via Debug mode, the same glitch will occur. However, Tails' tails will be present throughout most of the cutscene.