In TV Guide's spring preview roundup, they had a few Gotham teases that were pretty on-the-nose, which you could guess if you're an avid watcher of the show.
Jim Gordon, in the mid-season finale scene that mirrored the pilot, took Theo Galavan down to the docks. He didn't fake this death, though, like he did with Penguin. Instead, he outright murdered the criminal mastermind.
"He's certainly compromised," showrunner Bruno Heller told TV Guide. That means strained relationships professionally (with Captain Barnes) and personally (with Lee).
The biggest tease, though, was saved for the very end, as they said in no uncertain terms, "Bruce Wayne will finally find out who killed his parents!" Earlier in the season, Bruce came oh-so-close, after Galavan apparently had the data in question. The files were burned, though, so it's unclear how he'll find out now, nor what that will do to his overall mission of justice/vengeance.