In the Flashpoint universe, it’s revealed that Martha and Thomas Wayne survived the mugging with Bruce becoming the victim. This lead to Thomas turning into Batman and Martha into the Joker. She kidnaps the daughter of Harvey Dent and disguises Jim Gordon’s daughter like the Joker. Gordon shoots his daughter thinking it was Joker.
Eventually Batman went after the Joker and he could save the Harvey Dent offspring in time. When Thomas pursued Joker, she seemingly fell to her death.
However Martha survived and escaped. She took refuge in the hidden chambers under Arkham, where she heard the revelations from the Psycho-Pirate. With that information Martha developed a plan that would challenge all the things her husband Batman values.