In Mega Man #48, Madam Y and various X Corporation henchmen investigated the ruins of Wily Castle 3 searching for Dr. Wily. When her underlings reported that he had been found, she instructed them to take care of him, as Mr. X had plans for him. In the next issue, she is shown arguing with Gilbert D. Stern and Roslyn Krantz, the X Corporation having taken control of the Wily Castle claiming everything on it as theirs due to the organization owning the island, and not allowing the agents inside without a warrant. She also tries to convince them that the eight Robot Masters belong to them and were taken by Light Labs without permission, but the agents dismiss it.