Spoiler warning: Do not read on unless you’ve seen “Gotham” Season 2, Episode 13, titled “A Dead Man Feels No Cold.” 

The tragic saga of Mr. Freeze (Nathan Darrow) seemed to come to an abrupt end on tonight’s “Gotham,” with the scientist appearing to end his own life after losing his wife — but unbeknownst to Jim Gordon (Ben McKenzie) and the GCPD, the chilly villain survived his apparent demise, waking up with a frosty makeover in Hugo Strange’s (BD Wong) underground facility, Indian Hill, with an icy chip on his shoulder.

While Jim remains unaware of the forces that are building against him under the city — and right under his nose, if we count Edward Nygma’s (Cory Michael Smith) recent behavior — he has more immediate issues, namely the strain on his relationship with Lee Thompkins (Morena Baccarin) and the blackmail material that Penguin (Robin Lord Taylor) has on him, given his involvement in the murder of Theo Galavan (James Frain).

Variety recently spoke to McKenzie about the pressure Jim is under both personally and professionally as a result of his recent actions, and the new and returning villains we may meet in the second half of Season 2.

By the end of “A Dead Man Feels No Cold,” Jim believes Mr. Freeze is dead, but the audience knows that he’s just the latest addition to Indian Hill, and Hugo Strange is the puppetmaster pulling everyone’s strings. Will that storyline be a slower burn for the next few episodes, until we get closer to the end of the season?

I think the discerning audience member can realize that we’re heading in a direction where something’s going to have to give. Strange has been able to conduct his experiments pretty much in the dark — no one is really aware of it outside of himself and Ms. Peabody, and the monsters he’s creating are quite vicious, and you’ll see more of that as the season wears on. So eventually our hero is going to have to be aware of it, and I can’t give it away, but it will all make sense … I think the writers really have a wonderful way of bringing it all together at the end of the season, not just Strange and Gordon, but Strange, Gordon, and Bruce Wayne.

Penguin clearly harbors some resentment towards Jim over the consequences of Galavan’s death and where they’ve left him, and this week we saw Strange overhear a potentially damning exchange between them. With Penguin in such a precarious position, how will we see his relationship with Jim shift in the back half of the season?

Penguin has a big, wonderful journey this second half of the season. Really discovering much more of who he is, actually, as a human being, which does not just take a place in Arkham, or in Strange’s laboratory — it largely takes place outside of it. So as he’s figuring out more who he is, in a way that helps humanize Penguin even more, Jim is figuring out who he is in a darker, and nastier way. Even though they’re pulled the furthest apart they’ve ever been, in a way — because obviously Penguin blames Jim for his current situation in so many ways — they’re oddly coming back together, because they’re becoming more who they ought to be. What’s great about the origin stories is that we’re going to have so much time to watch these characters come together, come apart, come together, come apart, over and over and over again.

I’m guessing the introduction of Paul Rubens as Penguin’s father helps him on that voyage of discovery. What can you say about his role?

It’s fantastic casting; Paul is an absolute delight, and he’s wonderful on it. All I’ll say is it’s great. It’s really, really entertaining. The combination of Robin and Paul together, they’re just two peas in a pod, they couldn’t be happier together. It’s a wonderful plot line that does exactly what I was just talking about, allows Penguin to understand more who he actually is as a human being.

We’re currently seeing Bruce (David Mazouz) and Alfred (Sean Pertwee) tracking Malone independent of the GCPD, and Jim obviously has a few other pressing concerns on his plate in addition to solving the Wayne murders – when can we expect those storylines to intersect again?

This season for sure. We have not forgotten about it at all; it’s something that we felt we needed to give some space too, so that we could track Jim’s journey individually, as well as Bruce’s with Alfred, with the cave and all this stuff, but they will intersect again, and they’ll intersect in a fundamental way that really drives the season forward.

There’s obviously a lot that Jim and Bullock (Donal Logue) don’t know about what Ed Nygma’s been up to, but we’re starting to see his newfound assertiveness come out at the GCPD. How long will it be before they start to pay more attention to what’s bubbling under the surface there?

It takes a little bit of time. We draw it out just a bit so that Jim can get caught up in something that he believes is completely unrelated to Ed, but it may not be. We’re trying to make revelation of Ed as the monster he’s become as shocking to Jim and Bullock and the GCPD, as it would be, because he’s shown, to them, no outward signs of anything other than being a bit odd, and being a bit quirky. No notion that he’s murdered someone, and that he’s bipolar, really, which really hasn’t been explored.

I think one of the interesting things about “Gotham” is because it’s set in the “past,” of some sort, these notions of psychological issues where we would diagnose people immediately, like, “Oh, that person’s bipolar, that person’s this,” they go, “He’s kooky.” Only to have to come back and bite you in the ass. There’s a great conflict that we’re building towards with Ed and Jim, but we’re not quite there yet.

We’re realizing that it’s delicious for the audience to be so far ahead of Jim, seeing the villains in their private lives, and what they’re doing behind the scenes. It’s delicious for them to watch Jim get himself knee-deep in the muck, and have to figure a way out of it. To be completely unaware of how screwed he is, and then have to dig his way out — so we’re embracing that in the second season.

It’s a fine line to tread, because you don’t want to undermine Jim’s credibility as a detective when all these things are happening right under his nose, but at this point in the show, it makes sense that he wouldn’t be able to see the forest for the trees when he has so many other issues piling up on top of him. He’s not looking at the people closest to him, because why would he?

Yes, exactly. We’re trying to make it appear to come from so far out of left field, from Jim’s perspective, that he would have no real reason to suspect. He will stumble upon that later.

Episode 13 leaves Jim and Lee’s relationship in a pretty wrecked state — what’s ahead for them?

It’s a tragedy. The story we’re telling is a tragedy, and so the relationships are ripe for destruction. I think we’ve been able to find the real heart between Jim and Lee, that gives him more to latch onto in the world we’ve created, more than any other relationship, other than possibly [Jim and] Bullock’s. And so that will be, I think, an anchor for us moving forward, to understand Jim. But the truth is, in a tragedy you really only understand through loss. So they may, at some point in the future, get to a happy place, but clearly we’re presaging a downward spiral for them as well.

Does that loss untether him further?

Yeah, it does, because he’s been trying to be the man he ought to be for everyone, and in a strange way the killing of Galavan has unleashed these other sides in him, which do free him a bit. We talk about that all the time in the show, it’s kind of become a theme, that people need to find their true selves. And once their true selves are unmasked they are uglier than, quite frankly, any of us would want to admit, and that’s definitely true of him, and would be true of his relationship with Lee.

Anything you can preview about the introduction of Azrael?

I don’t think I’m allowed to. All I think I can say is that in the second half of the season you’re not going to lack for iconic villains in their new form.

Ditto on the return of Jada Pinkett Smith’s Fish Mooney?

If you spend a little time thinking about it, it all makes sense. [Laughs.]

“Gotham” airs Mondays at 8 p.m. on Fox.