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 7 more. He also aided Dr. Wily in repairing the recently discovered Shadow Man. (Mega Man #13-16)
Upon Flash Man's discovering of the Blue Chaos Emerald, Ra Moon expressed an interest in examining it, but was deny 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 one once and with help (alluding to Ra Moon). (#5)
Sometime after his capture, Dr. Light tries to discourage both Wily and Eggman from messing with the Chaos Emeralds due to both scientist having gotten in over their heads in handling with forces beyond their understanding. One of which includes Wily's attempt to control Ra Moon. (#9)