[Warning: Some spoilers ahead for season three of Falling Skies.]

Changes are afoot when Falling Skies returns.

Seven months following the events of the season-two finale, de facto leader Tom Mason finds himself president. Tom's sudden change of heart was just one of the developments that star and producer Noah Wyle grappled with. The other things? Dropping viewers into the action more than half a year later without any semblance of how things got there. One could argue that that is the mystery of season three.

"It was a pretty big gamble to embark on so many big storylines so quickly," Wyle admits in a chat with The Hollywood Reporter. "I had some apprehension about having left Tom at the end of season two not wanting any additional responsibility and turning down the presidency to suddenly finding him as the president."

PHOTOS: Broadcast TV's Returning Shows 2013-14

The ER alum credits executive producer Remi Aubuchon with finding a way to juggle multiple stories seamlessly. "He managed to craft and arc each of the storylines over the season in a gratifying way," he says.

TNT's sci-fi endeavor sees another dramatic shift with the 2nd Mass remaining relatively static this go-around, after two seasons leading a nomadic life. "To go from the 2nd Mass wanting to leave Charleston — disillusioned with [the town] — to suddenly committing to stay and forging an alliance with new aliens was also a big gamble," Wyle says, "as was the storyline with Tom's baby, the storyline with Hal and half a dozen other storylines we've kicked into play really quickly."

A lot is at stake for Tom and his counterparts this season: new alliances, the threat of a mole and a baby that may be trouble. In a chat with THR, Wyle speaks candidly about why season three is a "make-or-break season," the significance of the seven-month time jump and the slew of changes in 2nd Mass and Charleston.

The Hollywood Reporter: What's Tom as president like compared to the Tom that we've become accustomed to the past two seasons?

Noah Wyle: He accepted the role of president because he understood that to keep the population of Charleston calm and to keep everything from descending into chaos in the face of this new alliance, that they need to see some semblance of a civic structure. They're going to need to feel that there's somebody in charge, so it's more ceremonial, ritualistic. It's a pageantry presidency more than an actual presidency. He's very self-effacing about the whole thing. He doesn't really like being called president and he makes a quip about how he's the president of 20 square blocks, not really a nation. It's more of a strategic, psychological ploy than it is him embracing the mantle of leadership. That being said, I think as he begins to play this part, he realizes he's good at it and as the season unfolds, he grows into the role in a meaningful way. He goes from playing the president to being the president, to a certain extent.

PHOTOS: Summer TV Preview: 51 New and Returning Series

THR: Is there a decision that he has to make that catapults Tom to being the president instead of playing the part?

Wyle: We find out [something significant] midway through the season … that takes all the pressure off Tom.

THR: That's interesting, though. Is Tom more comfortable reporting to someone or being a No. 2?

Wyle: That was the way we set up the dynamic for Tom and Weaver [Will Patton]. The first season was all about the deconstruction of an intellectual. We took an academic and put him in an extreme situation where his skill set really seemed useless. At the end of that season, it began to dawn on him that being a teacher of students actually puts him in a better position to lead a young army than if he'd been a career militarist. The fact that he's a father actually gives him a sense of empathy and compassion in the way that Weaver's character doesn't, and Tom's ability to draw on historical parallels could be an asset in the way they forge strategy in battle. He starts to gain a little bit of confidence, and the second season builds on that as he embraces the role of second-in-command, and being Weaver's moral compass as well as his sounding board. In the third season, that dynamic is completely reversed where Tom's the power and Weaver's the advisor — it takes a while to get used to but eventually he does.

THR: Will Tom ever be comfortable in a position of power?

Wyle: I would like that to be what the final episode of the series is. I think that would be gratifying to see Tom go from somebody who studies the deeds of great and heroic men who've come before him to becoming the living embodiment of that.

THR: Anne's about to give birth to Tom's baby at the start of the season, but there's rumblings that the baby is ... different. What can you say about that added new wrinkle?

Wyle: Yeah, the baby's special. It was an interesting philosophical question to ask last season through these characters about whether it's cruel to bring in a baby into this world or whether it's a biological necessity, and if the species is going to continue they're going to have to propagate. So [Anne's pregnancy] answered that. On a personal level, it was really nice to see these two characters have a relationship — though they didn't fully commit to it yet because they didn't fully grieve the spouses that they lost when the invasion happened. Through this baby, they're able to make a commitment to each other and to a future together. This is the most fragmented that we've ever seen the Mason family. The boys have been clamoring for some independence and autonomy for years even though Tom's been reluctant to give them that and this is the season where he says, "You want it? You got it. Go do your own thing. You can't come crying to me if you have a problem."

THR: Is it a good thing that the Mason boys are off on their own this season?

Wyle: It's a necessary thing. I know I went through it when I was an adolescent, where you kinda have to go through the oedipal stages of killing off your father in order to establish yourself in your own right, so they have to as well. Ultimately at the end of the season they come back together as a family and realize that they operate well together. But it's a necessary stage of everybody's development to move apart for awhile.

THR: Hal is going through some physical hardships. How is Tom dealing with that?

Wyle: Yeah. He's paralyzed and schizophrenic ... There weren't a lot of scripted scenes between Drew [Roy] and I for the first half of the season, and that was intentional — to keep what he was going through a secret from his father. We establish very early on that there is a security breach — that someone's feeding information to the enemy — and the obvious suspect is the one with the eye bug. (Laughs.) That isolates Hal to a larger and larger degree. Hal feels that he could be culpable and he's not sure what he's up to. The only person he can really confide in is Maggie [Sarah Sanguin Carter] and that story reaches a climax in episode six. From that point on, Tom realizes what's happening and takes a much more proactive stance in figuring how to help Hal. But the first half of the season, everybody's doing their own thing and living autonomous lives.

THR: We've always seen 2nd Mass constantly on the move, but this season, they're staying put in Charleston. What are the challenges of making Charleston look and feel interesting?

Wyle: That's a tricky one. In the first season, we occupied a high school for four or five episodes and when we watched those episodes I didn't feel it worked very well. I thought there was something that dissipates the tension when this group is not on the move and not being hunted. We're going to lose some of this threat that we wanted to be ever-present. Second season we were on the move, we had a destination to get to, which gave us a great spine for the season: "We've got to make it to Grapes of Wrath California." Then we get to Charleston, it's not the Shangri-la we envisioned and we think about leaving and yet we don't so there's two ways of answering the question. From a production standpoint, it's easier to have the group stationary because two or three days of the week we can go on the soundstage for the cover sets. It's harder dramatically to maintain this sense of threat being ever-present. The way we negotiate that is by acknowledging there is a base and we're going to leave it a lot. We're going to go out into the field on missions, we're going to try to make contact with other resistance groups but we always have a home to go back to. I thought that worked pretty well for us.

THR: How significant is the reveal of the mole?

Wyle: It's pretty significant. It goes over the season and there are a lot of wonderful red herrings and twists and turns as we all try to figure out who it is.

THR: Since you have a producer credit, was it important for you to insert a season-long mystery like the mole?

Wyle: I like runners. I like things that reward an audience for paying attention and dropping clues here and there along the way. It was a hard secret to keep, knowing who it was and being asked on a daily basis by all the castmembers: "Is it me? Is it me? Is it her? Is it him? Is it Hal? It's gotta be Hal! No, it can't be Hal, it's too obvious!" (Laughs.) It's a good reveal [that comes around] episode eight or nine.

THR: Is there an episode that we should circle for Tom?

Wyle: There's a couple. There's one where Pope [Colin Cunningham] and Tom crash-land a plane. That's pretty interesting. There's another one that we filmed last but it may get plugged in as episode seven or eight. It's the first time where we really played with the notion of time and our own narrative structure. It was a big risk. [Moon Bloodgood's] stuff was particularly challenging because she was pregnant so we had about three episodes worth of Moon before she had to come back to California — but we wanted her to be in more episodes so we had to write scenes for future episodes that hadn't been written yet to shoot out of sequence. In that particular episode, there's a scene where she and I are in a room together and I have to look very different than I do on the show. We shot her half of it with a body double for me, while I stood behind a pillar directing the actor on how to move and when to move, and then three months later, we shot my side with a body double for her — and me trying to remember how Moon did it the first time so I could match it on my side. Yet when you see it, it's perfect.

THR: Physical transformation?

Wyle: I just had to be different.

THR: How far along are you in planning season four? (TNT has not officially renewed Falling Skies.)

Wyle: We just hired David Eick [Battlestar Galactica] to be our showrunner and we started staffing the writers room. I'm excited about going back to work. I feel like in a lot of ways season three was our make-or-break season. We had an OK first year; we didn't really know quite what we were doing but we did OK. Second season was better, but for the third season, we [were faced with making] the show that's going to be remembered for going three seasons or you make the show that's going to go on to five. We got over the hump and now I'm excited about how we can close this out in a satisfying way.

THR: How is season three a "make-or-break season"?

Wyle: Story-wise and creatively — knowing who these characters are, knowing what works well for us. It's a very odd dynamic because we've only done 30 episodes but we've been working on the show for four and a half years. It's a long time to have 30 hours of television — and it's a relatively short amount of time to have as many showrunners as we've had. We've had some huge changes on the creative team. It's a show that's had many fathers, but it has one godfather — and that's been the land of continuity. I'm curious to see what the next set of parents will do with this show under Mr. Spielberg's [who serves as an executive producer] watchful eye and to see where we can go with it.

Falling Skies returns with a two-hour season three premiere at 9 p.m. Sunday on TNT.

E-mail: Philiana.Ng@thr.com

Twitter: @insidethetube