This section of the history takes place during Flashpoint, a massive crossover event set in an alternate timeline to the mainstream DCU. History was completely changed when Professor Zoom finally found a way to erase his nemesis the Flash without harming his own legacy.
In the Flashpoint timeline, Joe Chill murders Bruce Wayne, rather than the boy's parents. Martha Wayne was so traumatized by the event and the loss of her son that she wasn't responding properly to therapy even after several months. Months after Bruce’s death, Thomas tracks Chill down and beats him to death. However, before doing do so, Thomas had talked to Martha, telling her that it was time to move on and that he missed her smile. While seemly despondent to Thomas telling her to move on, Martha took notice to the latter part of his statement. When Thomas returned and informs her that Chill was dead, she turned to her husband to reveal that she cut open her cheeks to create a faux smile, telling him that she was finally smiling. Thomas then had her institutionalized, realizing her mental breakdown.
Martha soon escapes and turns to a life of crime, working with her own version of Harley Quinn called Yo-Yo and becoming the archenemy of her husband, Batman. Her actions as Joker would cause further tragedy for Thomas as his vigilante partner Catwoman, to whom he had become a father-figure, was shot through the gut and paralyzed from the waist-down.
Martha later kidnaps the twin children of Judge Dent, and tricks Chief Gordon into shooting Dent's daughter by giving her the appearance of the Joker- complete with a a tape with a smile on it and and guns tied to her hands. After Gordon realizes what he has down, Martha ambushes him and slashes the chief's throat. Batman turns up to face his estranged wife. Thomas tells her he has discovered a way to rewrite history so Bruce was never killed, and about Barry Allen and how he helped him restore his powers. Martha, however, is shocked that her son will grow up to become her greatest enemy and commits suicide off a cliff near Wayne Manor. 
- 11 Appearances of Martha Kane (Flashpoint Timeline)
- 2 Images featuring Martha Kane (Flashpoint Timeline)
- 1 Quotations by or about Martha Kane (Flashpoint Timeline)
- Character Gallery: Martha Kane (Flashpoint Timeline)