Spoiler alert: Do not read until you’ve watched the finale of the second season of “Mr. Robot.”

What a long, strange trip it’s been. After a mind-bending second season of “Mr. Robot” that saw more than its fair share of twists, creator Sam Esmail delivered a finale that answered many of the lingering mysteries that have intrigued us all season long. We finally learned — chillingly — what Stage Two is, where Tyrell Wellick has been hiding all season, and the fates of Darlene and Cisco after the shoot-out at Lupe’s restaurant.

Naturally, though, Esmail raised just as many questions as he answered. Here, he breaks down the pivotal moments of the season two finale and tells Variety what’s in store for season three.

First of all, congratulations on Rami Malek’s win at the Emmy Awards.

It was fantastic and if I can speak objectively, the best speech of the night. He was great up there. It was funny, it was emotional, and it was really genuine. I kept telling him he was going to win. I don’t know why he was so surprised! But we were all really happy for him.

So Tyrell’s alive, and he is in fact real. But I’m not sure who was more surprised that Elliot got shot — him or the audience.

That is the point of that scene. I’m glad you brought that up. The whole time, whenever we talk about the show in the writers’ room and making the show, we always want the audience to be with Elliot. When he believes something, we believe in it with him. If Elliot’s confused about something, which he oftentimes is, we’re just as confused as he is. And if he’s in contradiction to us, which he will say to us, then we’re opposing him. I love the relationship we’ve created with Elliot. It’s a little unlike anything I’ve personally seen. I think it’s in a weird way its own dynamic and it’s allowed us to create these scenes where you can direct attention where you otherwise wouldn’t have if we didn’t have that offscreen relationship with him.

We finally find out what Stage Two is. It’s terrifying.

It is incredibly terrifying, especially given what just transpired over the weekend. It’s an interesting dilemma that we always put our characters in. Honestly, we want him to be the hero, but he’s doing something that a villain would do. Obviously it’s unbeknownst to him that he’s at the epicenter of all of it. We just thought what a great moral ambiguous ground to put Elliot in. And obviously it’s a thing that he’s battling internally within himself and with the world. It’s a great predicament to always find your main character in those crossroads.

Elliot seems horrified by it, but the plan has Mr. Robot’s fingerprints all over it.

It’s Mr. Robot from the get-go. We teased this volatile element of Mr. Robot in the beginning of the whole show. In the second episode, Mr. Robot’s solution to destroying the backup tapes at Steel Mountain was to blow up the power plant near the facility and that would destroy all the tapes. Being the other half of this personality, (Elliot) wanted to find a less volatile way. In the first season we saw that tendency inside him. And now that came to fruition in this season.

Tyrell sounds terrified, though, when he calls Angela. Why was he so scared?

Tyrell loves Elliot. The interesting thing about Tyrell and Elliot is that they have this bond, this connection. That’s what we set up in that first scene, actually the first time they met in the pilot. They have this relationship where they connect on this much deeper level. Tyrell’s set up as this villain but they’re not in this antagonistic back and forth. They actually have this weird deep bond. That was set up in that first scene in Coney Island when Tyrell tells this story about his father and not wanting to be like him. That resonates with Elliot, and Elliot at the time was Mr. Robot. The way we’ve presented Elliot’s real dad in the past, he was nothing like the Mr. Robot we see in Elliot’s split personality. And it’s a rebellion against everything Elliot’s dad was — a guy who was too weak to fight back against everything Evil Corp was. And Mr. Robot, the side of Elliot’s personality, connected with Tyrell’s rebellion against his father, the fathers they felt were too weak for them. There’s a real bond that formed there. In the end, when Tyrell shot him, he didn’t want to shoot him. He felt like this was a partnership that was on the verge of victory that they were going to complete this Stage Two. And Elliot was going back on it. When he shot him, he was literally in tears. That conversation when he tells Angela that he loves him, it’s true. From Tyrell’s perspective, he really does loves this person. He feels that he gives him the fulfillment that he’s always been looking for in his life.

Angela’s been an incredible journey this season, with her ever-shifting loyalties. Is she now working with the Dark Army?

The great thing about Angela, it reminds me a little bit of Jackie Brown, where we never knew what Jackie’s true motivation was. She was always playing both sides, and not until the end, did you finally reveal it. It has a lot to do with Portia Doubleday’s performance. You can just never quite read her. She does it in such an exquisite fashion that we played up the notion where she’s a character that’s riding down the middle. On the one hand, you could feel that she’s flipped and turned to E Corp, and on the other hand, no, she’s trying to bring them down. We played with that the whole season. We thought that was so fascinating. We’re double-downing. Our assumption by the end of the season was that she’s siding with the Dark Army. As we move forward to the next season, it’ll be interesting to play that dynamic. Is she really with them or is she not? It’s just something with Angela’s journey, we can always keep people off balance in terms of what directions she’s actually going in.

The one thing we’ve always believed is her love for Elliot. She tells Tyrell, “I should be the first person he sees when he wakes up.” Can we at least believe in that?

One hundred percent. I don’t think that will ever change. That’s one thing, as much as the plot machinations can always be a little overwhelming, we always try to ground everything in real human emotions and relationships and connections. Because ultimately this is a show about a bunch of lonely people struggling to connect, and when they do, that should feel very real and very grounded and one of the connections that’s always been very pure and genuine. From the start it has always been that connection between Angela and Elliot.

What did Whiterose say to Angela to convince her to drop her lawsuit involving the Washington Township documents?

I can’t tell you that. I’ll respectfully decline to answer. [But] we will learn one day, yes.

Darlene doesn’t get a chance to mourn Cisco’s death before she’s confronted with the unstoppable force that is Dom.

Portia, Carly (Chaikin), Stephanie (Corneliussen), Grace (Gummer) — all have been amazing this season. The one thing about this season is that everybody has been spread out, struggling to get their lives back in order. The one thing that we’re going to see a lot more in season three is some of these storylines colliding. And what that collision is going to look like. We started to see that in those scenes between Carly and Grace. That’s when fireworks happen. Because they’re both these amazing actors a the top of their game. I love shooting those scenes.

Dom gives Darlene that amazing speech about the “python approach” — it echoes her own approach to capturing her. That’s how she was playing her all episode, trying to get her to open up.

When I look at the whole second season, that whole python speech that Grace gives, I remember shooting it and feeling that’s what this whole season has been about. It’s been about all of these people lying in wait. With Whiterose and Angela, she explicitly tells her “I could have killed you 90 days ago but I didn’t.” And now with Elliot and Mr. Robot and the whole enactment of Stage Two. All of the storylines have been about these plans happening underneath all of our main characters without their knowledge. And it all paying off in the end. Dom says to her boss: her intention is to flip Darlene, to get the man in the middle, in this case, Tyrell. Season three, we’re going to explore if and how that would be possible.

We finally learn who’s been gaslighting Joanna — Scott Knowles, the CTO of E Corp. But she has her own nasty plan for him — framing him for murder.

The line in the last episode about of all the gifts, this is the greatest gift he’s ever given us, that was an allusion to this is the plan she’s enacting. It’s essentially a frame up job to get Tyrell off the hook for the murder. Scott fell right into her trap. Joanna, it’s hard. She can flip right on a dime. Stephanie plays it perfectly. She can be the sweetest and then she can be the harshest.

That coda at the end of the episode was a delicious nugget — not only do we find Trenton and Mobley, but Leon resurfaces, too.

We wanted to resolve all of the mysteries we’d been setting up all season, Trenton and Mobley their whereabouts being one of them. We find out they have gotten away, or so they think. And here comes Leon, who’s definitely an agent of the Dark Army. His intentions remain to be seen. We’ll definitely get into it in the third season.

One last question: I couldn’t help but notice the reference to classic USA taglines, from “characters like you aren’t welcome here” to “blue skies” to “Burn Notice,” in that interrogation scene. How did USA respond?

Can I just say that was done with pure love and USA knows that. When they read it, they thought it was hilarious.