Nanomachines are tiny computers that can be planted into a person's blood system and/or DNA.
Users of Nanomachines
Luna Moonstone: During the creation of Project Moonstone, nanomachines were added to the DNA of the project's first result. However judging on Dr. Eggman's words when talking to Luna about Project Moonstone's creation, it seems to apply that the nanomachines were eiter not intended to be added from the beginning, or they were added late in the project. Prior to losing them at the end of Death from Above Part 2, Luna's nanomachines would activate when her adrenaline gets to high. This causes her to lose control of herself and begin a rampage of murder. It was this outburst that caused the Chozo Species extinction and the deaths of 80 G.U.N. soldiers during the raid on the Space Coloney ARK.
Eve and Golden Darkness: According to Mega Man, two deadly assassins were created using nanomachines. When Team Mystery first met Eve, Mega Man reveiled that she was one of the assassins. And upon her debute, Golden Darkness was shown to be the second clone who also contained nanomachines.