[Warning: Spoilers ahead if you haven't seen the May 4 season finale of Gotham.]

The season finale of Gotham brought big changes to the city that will one day belong to the Dark Knight, but perhaps not changes that the audience expected: Marked-for-death crime boss Falcone (John Doman) choosing to retire in Florida, rather than stand up for his legacy? Butch (Drew Powell) shooting Oswald (Robin Lord Taylor) and Fish (Jada Pinkett Smith), giving the former a chance to kill the latter? Barbara (Erin Richards) trying to kill Lee (Morena Baccarin)? As showrunner Bruno Heller tells THR, "When you're telling a story that everyone knows all the characters and where they're going, you have to surprise people."

Even the writing staff of the Fox drama was thrown for a loop by some of the major beats of "All Happy Families Are Alike," according to Heller.

"We knew the season was the story of Penguin's rise to power, so that was always there," Heller says, "but how we got there was up in the air as we were writing it. So much of [the mythology] is laid out before you because of the future that everyone is aware of, but there are many things where, to keep a sense of life and things happening without the knowledge of history, we'd just tell the story and see how things unfold."

The same was true with Butch's indecision over whether to side with Fish or Cobblepot, and also with Barbara Kean's descent into madness. "The plot between Barbara and Lee came out of the show as it developed," says Heller. Although, as with the Penguin storyline, there was always an ultimate aim in mind when it came to Jim Gordon's former fiancee. "We always knew from the start that Barbara was the wrong woman for Gordon," he admits, promising that "we're going to see how [her attack on Lee] plays out" in future episodes.

Another character who underwent an unexpected change in the finale was Selina Kyle (Camren Bicondova), who went from street thief to gun-toting mole upon Fish's reappearance. Heller explains that that doesn't mean she's turned evil exactly — more that she's just a regular teenager. "Selina is one of those interesting Gotham characters in that she's ambiguous," he says. "It's still very much a story of a girl, not a woman, and teenagers try on different roles. She's still a protean human being. We're playing with that — she's not going to become one thing or the other definitively until she's a grown up."

Fans might be wondering what happened to Butch or Selina after Oswald's victory; Heller reveals that some moments in the finale were sacrificed for the greater good. "This world is so packed with incident and characters, it's difficult to tell the story you want in the time frame you have," says Heller. "There's an element of an overstuffed suitcase with all of these episodes, because there's so much to get in. You have to think of that as a virtue rather than a vice, because it's better than vamping because you don't have enough story to play with."

Something that did make it in was that final scene of Bruce Wayne (David Mazouz) discovering a hidden passageway in Wayne Manor. Is that…the Bat-Cave? Heller laughs when the question is asked. "It's a fireplace that moves sideways and goes downstairs," says Heller. "It's not the Bat-Cave, because the Bat-Cave only comes into existence when Bruce Wayne decides to become Batman. Call it his father's office."

What is in that office, and what it means to Bruce, will form much of the first part of the show's second season. ("It's very much a visualization of one's parents' secret lives, their past, when you're a kid that age," says Heller. "When you're so young, the idea that your father and mother had hopes and dreams and secrets of their own. That's what that staircase leads to. Dark secrets.")

Also on tap for the second season, he says, is more on Edward Nygma's descent into darkness, what Oswald does now that he's become Gotham's king of crime and the much-anticipated return of a character only seen briefly in the show's first year.

"We're going to find out how the hell Jerome, the proto-Joker we met earlier in this season, connects with the Joker as people known him. That's the big focus of the beginning of the second season. We're going to tell the story of how the Joker came to be," Heller says, before pausing and adding, "That's teaser enough, I think."