Gotham season three promises to be a very changed show, thanks to the machinations of Hugo Strange and the Court of Owls throughout season two. The Court of Owls, a secret organization controlling, well, everything in Gotham City, commissioned Professor Hugo Strange to run experiments to figure out the secret of resurrection, something he was eventually successful at to varying degrees.
While doing that, though, he also created a series of monstrous creations, and they escaped the Indian Hill facility in the season finale. In a bus driven (wildly) by Fish Mooney, the monsters got out into the city, and were freed from their imprisonment.
"The nature of the city of Gotham will change," EP John Stephens teased of the release of Strange's monsters to TVLine. Those monsters include the second character played by David Mazouz, whom we've speculated on considerably and Stephens teased only is "a development that is in line with all the other story we've been telling, but one piece that we've kept hidden," which seems to point even closer to him being Thomas Wayne, Jr. and having a direct connection to the Court of Owls, as we previously deduced.
As for some of the new villains, the heavily-teased Mad Hatter was also confirmed as arriving next season, after an Easter Egg saw Hugo Strange reading a tale of Alice when deciding what personalities to imprint on some of his subjects. There will also be a young female villain added "who uses her sexuality to entrap men," which sadly describes about 90% of female villains in superhero comics ever, so it's hard to narrow down.
Gotham Season 3 will air this fall Mondays on FOX.