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.
Madam Y is one of several characters who was designed by Hideki Ishikawa and included in a piece of artwork (shown here) depicting an alternate version of the Mega Man universe. Ishikawa referred to her as an unnamed secretary, with an apparent association with Wily indicated by the letter W on her outfit. The Archie Comics version of the character sports a Y instead.