While Dr. Wily was investigating the Lanfront Ruins, Ra Moon took control of his laptop to use it in recreating his recently destroyed Robot Masters, as well as creating seven more. He also aided Dr. Wily in repairing the recently discovered Shadow Man. (Mega Man #13-16)
Upon Flash Man's discovery of the Blue Chaos Emerald, Ra Moon expressed an interest in examining it, but was denied the chance as Wily wanted him to create a Met Rice Cooker.
After defeating Copy Robot and the Genesis Unit, Mega Man and Proto Man explain to Sonic and Tails that Robot Masters can't be rebuilt easily due the complications of the I.C. (Intergrated Circuit) Chips which are the source of the robots' personality. Proto Man explains that Wily only did so once, with help (alluding to Ra Moon). (#5)
Sometime after his capture, Dr. Light tried to discourage Wily and Eggman from messing with the Chaos Emeralds by bringing up how both scientists tried to handle forces beyond their understanding only to need saving. One of which included Wily's attempt to control Ra Moon. (#9)