When Joss Whedon wrote and filmed the post-apocalyptic Dollhouse episode "Epitaph One," it was entirely possible it would be the final episode in the Fox series.

So when Fox picked up a second season of the sci-fi series, Whedon instead intended to use the "Epitaph" storyline as the jumping-off point to drive the new season’s arcs. But the episode ended up only on the season-one DVD/Blu-ray set (it also screened at Comic-Con), complicating any plans to use it to inform the second season’s stories.

Nevertheless, Fran Kranz—who plays doll programmer Topher—confirmed that producers still plan to go there, even though there’s a part of the audience who only watched the episodes that aired on Fox last season. (Possible spoilers ahead.)

"We’re really going to move forward towards where ’Epitaph One’ ended, and we’re heading towards the apocalypse," Kranz said in an exclusive interview Thursday at the Television Critics Association summer press tour in Pasadena, Calif. "It’s still going to go according to [Whedon’s] plan."

"Epitaph One" takes place in the year 2019 in what appears to be a Los Angeles ravaged by some kind of apocalypse. Survivors, led by Felicia Day’s Mag, discover the abandoned Dollhouse underground. Flashbacks fill in the period between our time and 2019, suggesting that the technology developed by the Dollhouse has led to massive mindwipes and identity replacement, culminating in war and chaos.

Though the episode never aired, it will inform the new season, Kranz said. "Felicia, her character and her world, is in the first episode of season [two]," he said. "So we’re sticking with it. Things could change. We could always play it out a little differently if we wanted to, but that’s the trajectory we’re on. My character kind of loses his mind in [’Epitaph One’], feeling the weight of what he’s done—the technology he invented destroying the world—and he kind of feels bad about it. We’re kind of already heading there in the second season."

Even without jumping ahead, Topher has a lot to answer for when Dollhouse returns. Dr. Saunders (Amy Acker) learned she was a doll, whom Topher programmed to hate him.

"In season two, we address that pretty much immediately," Kranz said. "Dr. Saunders—Amy Acker and I, who’s the best—we work across the hall from each other, so we can’t avoid each other. All that kind of awkwardness ensues, and it gets pretty dark. I have to answer to her eventually. That’s going to be really exciting. Right now, Topher’s a little down on himself, and he’s starting to think like, ’Wow, one of the most beautiful things I created hates me. Maybe I’m a bad guy.’"

That certainly indicates that Topher is still on a dark path that could lead to the apocalypse of "Epitaph One." "Look, it’s a provocative show," Kranz said. "The technology, when you really choose to think about it and its consequences, is really provocative. We’re definitely exploring that much more this season."

The second season represents one last chance for Dollhouse to capture a sizable audience. "It’s like second life, and we’re really going for broke in the second season," Kranz said. "It’s really going to be out there. It’s really twisted. It’s much darker. We’re really taking advantage of the opportunity, so I’m pumped. Certainly it’s getting more into the characters. They’re no longer really stand-alone [episodes]."

Dollhouse returns Sept. 25 at 9 p.m. on Fox.