At the end of season one of Gotham, it seems as though Fish Mooney, a mobster climbing her way to the top of the criminal underground, met her end after falling into the water, never popping back up. However TVLine reports that Jada Pinkett Smith, who portrayed Mooney, signed on to reprise the role.
Showrunner Bruno Heller hinted after Mooney's apparent death that nothing is as it seems. Smith signed on for multiple episodes during the second half of season two, so chances of her appearance being a flashback are pretty slim. Mooney does have some unfinished business on Gotham as there are plenty of people who have wronged her, including Penguin and those in charge of running the experiments on Indian Hills.
There's no news yet on when Fish Mooney will reappear on the show, but the second half of season two of Gotham comes back to Fox on Monday, February 29.