“Marvel’s Agents Of S.H.I.E.L.D.” Season 2, episode 3 finally went inside Hydra. After fighting them for Creel (Brian Patrick Wade) and losing the original 084 to them, S.H.I.E.L.D. finally got a leg up on the terrorist organization -- but it came at a price.

This episode caught up with the real Jemma Simmons (Elizabeth Henstridge) -- as opposed to the hallucination version of her that Fitz (Iain De Caestecker) has been talking to. Simmons started her day in a nice house and went to an office building that turned out to be Hydra. Simmons is now a biochemist for Hydra… but don’t worry, it’s just a long term, undercover mission.

She realized that the lab work she was doing involved someone she knew. She saved Donnie Gill (Dylan Minnette) in “Marvel’s Agents Of S.H.I.E.L.D.” Season 1, and now Hydra wanted him back. His power to freeze things could be useful. She told Coulson (Clark Gregg) about the new discovery, and he advised her to make friends at Hydra. She needed some people who trusted her so they could get more information.

It was a little hard for her to make friends when armed guards took her to the dreaded "upstairs." Bakshi (Simon Kassiandes) admonished her for not telling them about her history with Donnie. He questioned her alliances, but Simmons said that she was with science. She was loyal to whoever had scientific resources. Bakshi determined that she would go with them to Morocco to find Donnie.

S.H.I.E.L.D. was going on their own mission to get Donnie. They needed to get to him before Hydra, but they left Fitz behind. He was still having trouble with words, and he couldn’t give them helpful information on Donnie even though he was closest to him. Fitz decided to sulk about being left behind in the basement and found Ward’s cell.

Fitz was shocked to see Ward (Brett Dalton). Apparently, he didn’t know that Coulson was keeping him so close. Fitz unleashed his frustrations on Ward. “Despite all of this, it’s really good to see you,” Ward said.

However, Fitz was having a breakdown. Ward explained that he wanted to save Fitz and Jemma. Releasing them into the ocean was the only thing that gave them a fighting chance. Fitz decided to show Ward what he and Jemma went through. He deprived the cell of oxygen until Ward decided to give him some crucial information. Ward told Fitz that Hydra has already brainwashed -- or "programmed" -- Donnie and they’ll just re-trigger his programming. Fitz got Mack’s (Henry Simmons) help and they got in touch with the team.

They found him on a Hydra boat where he had created a small iceberg. He wanted people to stop coming after him. Simmons tried to be gentle and just talk to him. Simmons started repeating what Bakshi was saying through her earpiece. It was triggering his programming, but she didn’t know that.

Hunter (Nick Blood) found Donnie and saw him talking to a Hydra agent. Hunter put his target on her back, but he didn’t know that Simmons was a double agent. May saw Simmons and shot Hunter in the arm to save her.

They maintained Simmons’ cover and Bakshi finished re-triggering Donnie’s programming. He ordered Donnie to freeze the whole ship and everyone in it. Skye (Chloe Bennet) was in a sniper position and killed him, something she has never had to do on a mission before. She took another shot near Bakshi and Simmons to make them run, and Simmons pushed him out of the way of the shot.

Bakshi told Whitehall (Reed Diamond) that he wanted to bring Simmons upstairs. He trusted her after she pushed him out of the way of Skye’s bullet. He reminded Whitehall that if she failed to comply, they could always brainwash her as they had Agent 33 (Maya Stojan). The agent was seen strapped down with her eyes held open early in the episode, but now she happily brought files to Whitehall. Clearly, their brainwashing worked.

Skye went back down to Ward and asked if he had been brainwashed by Hydra. “I wish I could say that’s what happened, but I swore not to lie to you,” he said.

She didn’t understand why he was so focused on rebuilding the trust now. “I know something,” Ward said. “And I want you to believe me when I say it: Your father is alive. He’s looking for you, and someday, if you let me, I’ll take you to him.”

“Marvel’s Agents Of S.H.I.E.L.D.” Season 2 airs Tuesdays at 9 p.m. EDT on ABC. Do you think Skye will let Ward take her to her father? Sound off in the comments section below!