Secrets were finally revealed in “Marvel’s Agents of S.H.I.E.L.D.” Season 2, episode 20. Coulson (Clark Gregg) was able to get along with Gonzales (Edward James Olmos) and the new S.H.I.E.L.D. team once he revealed what he had been hiding. He was actually helping save the world. 

The episode started with a flashback to one year ago. Coulson secretly met with Sam Koenig (Patton Oswald). Sam mentioned that Hydra likely took out Gonzales. However, Coulson was really visiting Sam to see something Fury wanted kept under wraps. Sam opened up a door and showed Coulson the helicarrier that fans who saw “Avengers: Age of Ultron” will recognize.

“I gotta tell you, it’s not easy keeping something as big as a helicarrier a secret,” Sam said.

Theta Protocol was the helicarrier that the Avengers used to save Sokovia. Fury wanted something completely off the books after the fall of S.H.I.E.L.D., and that’s why Coulson couldn’t tell anyone.

Coulson told the council what he was up to, and it certainly helped earn some trust. After all, he technically just saved an entire country of people from being killed by robots. Coulson offered to merge the two S.H.I.E.L.D. organizations. He would act as director under the advisement of the board. Gonzales agreed and said a helicarrier couldn’t help their biggest problems: people with powers.

Skye (Chloe Bennet) was in the infirmary, sitting by Lincoln’s bedside. As he regained consciousness, he was scared. He told Skye that they couldn’t trust S.H.I.E.L.D., but Skye promised that they could.

Meanwhile, Raina (Ruth Negga) was adjusting to her new powers. After her vision of Sokovia, she realized her powers were truly a gift. She revealed that she saw “a giant stone, but not a stone.” It also looked like an ocean. Jiaying (Dichen Lachman) revealed it was a device her ancestors spoke about. The Kree created it to destroy the Inhumans.

Gordon (Jamie Harris) teleported Raina onto Gonzales’ boat. Hunter (Nick Blood) caught them and alerted everyone. Bobbi (Adrianne Palicki) and May (Ming-Na Wen) caught up to them, but Gordon teleported Raina out before they could fire their guns.

In the short time they were there, they confirmed Raina’s vision. They found giant stone that turned into liquid and back into a stone. When Jiaying heard about how easily Gordon followed Raina’s lead, she asked Cal (Kyle MacLachlan) about the new Inhuman. Cal noted that she was good at convincing people to give her what she wanted. It left Jiaying concerned.  

Back at S.H.I.E.L.D. headquarters, Coulson questioned Skye about the break-in. She said that neither her nor Lincoln knew about the weapon. Coulson wasn’t sure they could trust Lincoln or any of Skye’s new friends, but Skye promised him otherwise. May reasoned that a man who could teleport was dangerous, but Skye said May was just as dangerous. She brought up the Bahrain incident where May killed a little girl who was Inhuman, and May wasn’t very responsive after that. Skye promised that the Inhumans just wanted to be left alone.

Yet S.H.I.E.L.D. wasn’t going to just let them live without a confrontation. Gonzales revealed to Bobbi that they figured out how to track Gordon’s teleporting. He wanted to pay the Inhumans a visit, but Coulson wanted to avoid a war. He convinced the council that they shouldn’t go in guns blazing. They should use Skye as a liason and start with a simple conversation.

Skye wasn’t happy that agents were going to Afterlife. “You know how this works. You’re a S.H.I.E.L.D. agent,” Coulson said.

“I don’t know what I am anymore,” Skye said. However, she promised that she and Lincoln could get Jiaying to listen. She revealed to Coulson that Jiaying would listen because she is Skye’s mother.

Raina didn’t want Jiaying to meet with the organization. She had a vision that S.H.I.E.L.D. would attack Afterlife. She claimed that Jiaying couldn’t meet with S.H.I.E.L.D. or else the vision would come true. Raina suggested to Gordon that she should do it. Gordon went to Jiaying and revealed what Raina was trying to do. The leader had Raina kept under close watch until after the meeting.

Jiaying talked to Cal and asked how they could convince the agents that the Inhumans meant no harm. Cal said that they could give him to S.H.I.E.L.D. “Let me protect my family the way I couldn’t before. Please,” Cal said.

Skye asked Jiaying to meet with Coulson. “Please, Mom,” she said. Jiaying gave in, but Coulson wasn’t the one meeting with her. Gonzales said that Coulson couldn’t go. The council, including May, decided that he was too close to the situation.

Gonzales met with Jiaying, and Skye took Cal out to the agents. The father and daughter shared a sweet moment and said that they were glad that they finally got to know each other. However, Cal wasn’t going in quietly. The agents found empty vials on him, and he refused to tell them anything about what was in the containers. It was the concoction he takes that makes him super strong.

Back in Jiaying’s office, Gonzales gave Jiaying a box with a necklace in it. It was a traditional Chinese charm that wards off evil spirits. S.H.I.E.L.D. found it at one of their investigation sites and Jiaying revealed that she had planned to give it to Skye. Jiaying was happy to have it back. Gonzales said that they only wanted to protect everyone. However, S.H.I.E.L.D. would take care of anyone who disturbed the peace.

Jiaying didn’t want to be cataloged and watched forever. She was insulted by Gonzales’ plan so she brought out a diviner that the Inhumans made. “Let’s hope you’re one of us,” she said as she broke the crystal. The mist turned him to stone. Jiaying then shot herself twice with his gun before coming out of her office, where everyone could see her. 

“He tried to kill me,” Jiaying said. “S.H.I.E.L.D. tried to kill me. This is war.”

Elsewhere in episode 20, Mack turned in his badge and quit working for S.H.I.E.L.D. He said that he still didn’t believe Coulson was able to run the organization after being brought back from the dead by alien blood. “You can’t be blamed for what happened to you, but you can’t be trusted either,” he said.

He has pretty unfortunate timing since he quit just before one of his best friends was taken hostage. Bobbi and May were flying the first plane in for the mission -- but it wasn’t really May. It was Kara (Maya Stojan), who used the mask to escape her cell and fool everyone.

The former agent said that she remembered what happened with Bobbi before Hydra brainwashed her. The two fought, and it looked like Bobbi won. The plane landed and Grant Ward (Brett Dalton) put a tranquilizer bullet in Bobbi.

Ward and Kara were keeping Bobbi unconscious in the plane. Kara asked why they weren’t killing the agent, and Ward explained, “Closure is about so much more than that. It’s about digging in, doing the work.”

Earlier in the hour, Simmons (Elizabeth Henstridge) revealed that she wished she had killed Ward. She claimed whatever awful thing he did next would be on her, so it looks like she has quite a guilt trip ahead of her.

“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 side with her mother or S.H.I.E.L.D.? Sound off in the comments section below!