As promised, "Marvel's Agents of S.H.I.E.L.D." closed out its third season down an agent and, somewhat unexpectedly, a villain.

In the two-hour season finale, the team took drastic measures to put an end to Hive and his deranged plans. But while virtually all the agents experienced brushes with death, ultimately it was Lincoln who perished, sacrificing himself in order to launch Hive -- and an armed nuclear warhead -- into deep space. This, of course, devastated an already emotionally unstable Daisy, who crumbled to the floor as Lincoln's last words reverberated in her ears -- "I love y--."

"Agents of SHIELD's" Brett Dalton Explains Hive's Major Season Finale Moment

CBR News spoke with "Agents of S.H.I.E.L.D.'s" executive producers Jed Whedon and Maurissa Tancharoen about the epic finale, and what it means for the team as they prepare for life after Brett Ward/Hive and Lincoln. The pair discussed how truly difficult it was to say goodbye to Brett Dalton and Luke Mitchell, both as actors and the characters they portrayed, and how the ramifications of Lincoln's death will lead to Daisy going rogue in Season 4.

CBR News: How difficult was it to say goodbye to Brett Dalton and Lincoln Mitchell?

Maurissa Tancharoen: It was so, so hard. There were many tears. It was very emotional. Even in the process of developing their arcs and breaking the season, it was a decision we struggled to finalize. We knew that we had to, though. We had to close a chapter with Ward. To sustain an antagonist for this long or to go beyond three seasons -- we just didn't want it to lose any steam. At our wrap party, there were several emotional speeches being made for both of those guys.

Jed Whedon: One of the things about television is that it's fluid. You always have to generate a lot of different stories. Sometimes you eliminate a character and it's easy, because you either don't like the person or you don't like the character. This was a situation where we didn't have that. Both of these actors are just great guys, they're great to work with and are pros. It was a very emotional end of the season for everybody.

Tancharoen: A week before we wrapped, we were here at home. I was thinking of Brett and Luke. They are such great people, and so talented and so handsome. "Oh, my God. What have we done?"

After watching Ward evolve from a member of S.H.I.E.L.D., to Hydra agent, to Hive, why did it feel that this was the time to let him go?

Whedon: One of the reasons we closed that chapter was to start a very different, very new chapter next year. We're very excited about it, but that's as specific we can get.

Now that viewers have seen the finale, what were the most important aspects, to you, about the send-off you gave Ward/Hive?

Whedon: Hive revealed his motivation: "I want a connection." That's a fitting end to his story. Also, to Ward's story, he wanted that with Skye. Now, here he is, sitting with Lincoln, the one person who had that with Skye/Daisy. There's some poetry to the simplicity and the quietness in that moment that we loved. It was a fitting end for someone with [goals of] world domination, and to our buddy Grant Ward, who we managed to maintain as an antagonist for three seasons, which is a lot for one character.

Tancharoen: There's a sort of simplicity to [his grand scheme]. He had this great plan to transform humans into Inhumans, all over the world. At the very end, when Hive is meeting his end, he says, "I'm finally going to experience something that has eluded me all these years -- and that's death." There's a simplicity to it in that, it's quiet. It's just the two of them, and he said all he wanted was to make the world better. He just wanted a connection.

How will the rest of S.H.I.E.L.D. deal with the loss of Lincoln?

Whedon: It's safe to say they were emotionally affected by it. When we come back, we'll get a sense of how it's affected their plan moving forward and the way they operate.

Earlier in the finale, Daisy begged for Hive to take her back. How did that weakness sit with her afterwards?

Tancharoen: She's obviously broken by what she did. Her addiction to Hive and his sway are so powerful. She does her most unforgiving act in trying to go back to him.

Whedon: It's a mixture of many things. She's riddled with guilt. She's ashamed for her weakness in going back to Hive. In that moment, where Lincoln basically calls her out on it -- he's sitting there bleeding out from his stomach and he says, "I know why you really went back." That's too much for her to handle. To have Lincoln sacrifice himself for all of her sins, as she says, it's going to be hard for her to recover from that.

In the aftermath, Daisy seems to have found a new purpose. What is it, exactly, and how does it run in opposition to S.H.I.E.L.D.?

Whedon: We'll have to wait to see on some of that. I think it's safe to surmise from the end that Daisy is still trying to make good on her promise to protect these people. But, Daisy is also trying to make good on what Lincoln believed in her. He says at the end, "I really believe you're meant for more than this." I think she's trying to make his death not meaningless.

With all that said, she's obviously doing that in a different way, and with a lot of destruction in her wake. When we come back next season, we will see what her modus operandi is and what she believes about the team and S.H.I.E.L.D. as a whole. I think she's back to being a loner, now.

The closing moments of the finale introduced us to Dr. Radcliffe's artificial intelligence, AIDA. In what way are you putting a spin on the A.I. trope?

Whedon: Radcliffe has a good heart. He just puts his foot in his mouth and will do anything for science. As he says at the end, "A lot of people died. Maybe they didn't have to." He thinks he is doing good. Whether or not that proves to be true, we'll see.

Tancharoen: He's modified himself. He has that prosthetic eye, and we met a woman who he put a little screen within her arm. This is something he's been exploring for a while. Perhaps he believes this is the next step in human evolution.