After the defeating two of the eight bosses in MMX3, Dr. Doppler orders the Nightmare Police to capture X for him, alive if possible. After the defeat of Bit and a few more bosses, Byte will appear as a sub-boss in the stages until he's defeated. If he's defeated without using his weaknesses, he will retreat, dying only if he's defeated with Tornado Fang or Ray Splasher. If Byte survives, X will have to face him and Bit again in the first Doppler stage, where they will combine into Godkarmachine O Inary. If only Bit or Byte survive, they will still be able to transform into Godkarmachine O Inary.
- Repellant Hand - Byte launches one of his hands and it sticks to the wall. While the hand is attached, X will be unable to wall-kick on that surface.
- Launch & Ram - Byte slams into his opponent and then delivers a powerful wind-up punch.