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Agent Garrett is casually flying, reading a book when two planes pull up beside him. He radios to see if friendly but quickly learns they are not as they fired two missiles at him. Through some evasive maneuvers, Garrett avoids them but realizes the attacking planes are S.H.I.E.L.D.
Still at an emotional stand-off, May finally kicks her gun away and explains the phone she was using was a direct line to Director Nick Fury. She also has no idea where the plane is headed, but stated HQ can override the controls. May asks Fitz what he needs an encrypted line for, and admits that she and Coulson have also been keeping secrets, but the line he wanted to use was to contact Simmons about Skye’s blood sample. Coulson tells Skye to get to her laptop and find out where they are going.
At The Hub, Simmons works on the blood sample. She is interrupted by Agent Triplett, and she quickly turns off her computer. Triplett asks what she is doing and mentions helping her and her team getting the formula to Skye. Simmons closes the door and states that she’s hit a dead end on research, wanting to call a person at the academy for help. Triplett goes to get a secure feed so she can make the call.
Skye tries to log on to the system but states everything is encrypted. As Coulson asks May what is going on, they receive a transmission from Garrett, who still can’t shake the drones that are after him. Coulson ices May, and sends Fitz to bypass their weapons so they can use them, and Skye to hack through the signal. He then drags May into the confinement room with Ward.
Fitz is able to bypass to use the ship’s guns to help Garrett. Coulson takes down both drones.
At The Hub, Agent Hand and her team see the drones are taken down. They think about taking down the bus, but realize Garrett is with them too, and decide to take them all in. Agent Shaw states he has a hard time killing the people he considered friends. Agent Hand states that once that encoded transmission went out, everything changed. She states that their allegiance is being tested today, and if wavered, you will die.
As Skye works on decoding the signal, Garrett comes aboard and Coulson states he thinks Agent Hand is The Clairvoyant. Garrett can’t believe it, and tries to argue the point with Coulson. Skye cracks the code and a message appears: “Out of the shadows, into the light,” and the last word in the message decodes and spells “Hydra.”
Coulson and Garrett deduce that Hydra has infiltrated S.H.I.E.L.D. at the highest levels, and the message was sent out for people working for Hydra to come out and take over. They decide they can’t do anything else but take a chance on facing them at The Hub, and saving Simmons and Triplett.
Agents in battle gear take away prisoners at The Hub. Agents tell Hand that they can’t find Simmons and Triplett. Hand tells them to go find them.
Simmons gets through to Agent Weaver at the academy but, before she can ask anything, Weaver states they are under attack, and to not trust anyone. The signal goes dead, and Triplett locks the door. Simmons looks at him nervously, and he pulls out a knife. He then hands it to her and states if she stabs him, he knows he can’t trust her.
May wakes up and Ward grills her about going behind the team’s back reporting to Fury. She states that he let his emotions get the best of him killing who he thought was The Clairvoyant, realizing it was Skye, not the team. Then states he shot the wrong person anyway. Coulson comes in to have May call Fury.
The bus lands at The Hub, and May tries the line to call Fury, and is met with a voice she does not recognize. When she asks for Fury the voice states he’s dead. May is shot and the bus is being breached.
As Coulson patches up May, she admits that she has been reporting to Fury about any changes in his condition, physical or mental. Coulson realizes she knew about T.A.H.I.T.I. May states she and Fury came up with the plan for the team, and Fury then gave Coulson the parameters to assemble the team, knowing he would recruit May for the job. May confesses that she has feelings for him, and that she was trying to protect him.
They all meet in the conference room and Ward states that Hydra can’t know about all the data they have on the weapons and people they have encountered. Skye is backing up the system onto a hard drive, then wiping the system clean.
Inside The Hub, Simmons and Triplett are found by the agents.
Inside the bus, the team are underneath the main deck. Skye hands Ward the hard drive, stating it will be safer in his hands. Coulson tells Ward and Skye to disable the lock that HQ has on the plane, while the rest go to free Simmons and Triplett.
Simmons and Triplett are met by Agent Hand. She states Hydra have taken over S.H.I.E.L.D. at the highest levels, and that those who resist, including Fury, have been eliminated. She tells them that they either swear allegiance to Hydra, or share Fury’s fate. The other agents point their guns at them. Simmons nods to Triplett who quickly disarms one of them, and Simmons tosses the knife to him. Hand then states that was the right answer, revealing she is not with Hydra. Simmons is relieved but Hand is quick to note that Coulson is part of Hydra.
Coulson, Fitz, Garrett and May fake out guards and reach the video surveillance room of The Hub.
Agent Hand tells the agents to find Coulson and the rest of the team, realizing they are hiding somewhere in The Hub. Simmons tries to argue that Coulson is not part of Hydra, but Hand is quick to dismiss it, listing a charge of crimes Coulson has made by disobeying orders.
Skye and Ward are surrounded by agents outside of a closet they are hiding in. Ward states he can take out the agents, giving Skye a clear path to the processing room. She says it’s a suicide mission, and Ward states maybe he deserves it, considering he shot the wrong person. He tells her he shot him to protect her. He tells her if he survives, he wants to open up to her. She kisses him stating just in case he doesn’t make it. Ward is able to clear the way, then asks Skye if she’s ready to hack the system. She opens up her backpack showing a large brick of C4, stating who said anything about hacking.
The team can’t find Simmons on the surveillance cameras, but they see Agent Hand. Garrett states they need to go through the ventilation to reach Hand, and take her out. Coulson states they can’t just kill her, but Garrett is insistent about her being too much of a threat. Garrett lists all the bad things The Clairvoyant has done, including having Quinn shoot Skye and brainwashing Raina in the memory machine. Coulson realizes he never mentioned that about Raina to him. Agents storm in with guns drawn and Coulson tells them to arrest Garrett because he is The Clairvoyant. Garrett says he knows some of them have orders from Agent Sitwell, and three of the agents take out the rest, revealing they are with Hydra as well.
Garrett reveals Hydra has been inside S.H.I.E.L.D. at the highest level the entire time. He tries to recruit Coulson but realizes he will have to kill him and May. He offers Fitz a job with Hydra, or to be tortured and work for Hydra anyway. Just as he’s about to have his men shoot, Ward and Skye blow up the processing room, knocking out the lights, and when the reserves come on Coulson and May fight the agents. With help from one of Fitz's gadgets, Coulson knocks out Garrett. Agent Hand and her agents come in, stating she’s heard everything, revealing a hidden microphone in the room. Coulson asks how deep did Hydra go. As Hydra are being taken away in handcuffs, Triplett and Ward are shocked to learn their S.O., Garrett, was The Clairvoyant.
Hand explains Captain America has destroyed the helicarriers at the Triskelion but has disappeared. Hydra factions have taken control of at least two major S.H.I.E.L.D. bases and Hand will be operating from the Fridge. Ward volunteers to lock up Garrett personally, blaming himself for not seeing through Garrett's deception. Hand agrees to take Ward with him and leaves Coulson in command of the Hub, warning him that they may be the highest-ranking S.H.I.E.L.D. agents that aren't compromised or dead.
On the Bus, Skye looks at her recently-assigned S.H.I.E.L.D. badge while her teammates survey the damage to the plane. Coulson comes in and puts them to work repairing the plane. May wonders if he still wants her there, and Coulson says that she's an ally even if she isn't a friend.
Hand, Shaw, and Jacobson load Garrett aboard a plane and fly him to the Fridge. En route, Ward watches as Hand tells Garrett that they'll put him deeper underground. She asks Ward if he wants to shoot the real Clairvoyant. After a moment, Ward stands up and takes out his gun, shooting Jacobson and Shaw, and then Hand. Garrett smiles in satisfaction and Ward nods to him.