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Zooming through the sky in his S.H.I.E.L.D. plane, Garrett encounters a couple other jets. They fire missiles at him, which he out-maneuvers causing them to detonate each other. He soon notices that these planes trying to shoot him down are S.H.I.E.L.D.
On the bus, Phil tries to find out from May where the plane has been rerouted to and why she had an encrypted phone line in the cockpit. She admits that she has nothing to do with the change of course and that the tapped wire was there in order to communicate with Director Fury. She asks Fitz why he was tampering with the wires to begin with. He divulges that he was trying to communicate with Simmons at HQ. Fitz allows Skye to enter the lab, in order to track the plane's destination. Coulson asks who Simmons is communicating with in order to see if she is safe.
In a lab at the Hub, Simmons is running tests on samples of Skye's blood. Agent Triplett enters asking if she's busy. Though she says she is, he still proceeds to talk to her. When he tries to see what she is working on, she quickly turns off her computer monitor. After she closes the door, she decides to tell him about her blood scans, but asks for it to be a secret. Because he has level 6 clearance, he can access more information in order to help Jemma.
On her computer, all Skye is able to pick up is an out-of-the-ordinary sonic signal. They pick up a transmission from Garrett who requests that they shoot his pursuers out of the sky. Coulson shoots May with an ICER to knock her out and he and Fitz carry her to the interrogation room where Ward is still contained.
Fitz begins running cables to power up the weapons towers. Using aerial tactics, Coulson takes out the rogue agents. In the Hub mission room, Agent Hand and her men decide not to send out more drones but to let Coulson and Garrett return to HQ. One agent expresses compunctions for killing men who were on their side.
Skye works on decoding the strange signal, and the agents believe Victoria Hand is the clairvoyant. Garrett tries to convince them that he isn't but he gives in after the transmission is decoded: "Out of the shadows into the light... HYDRA".
Despite of the uncertainty that might be awaiting them at the Hub, they still decide to stay aboard the plane to save Simmons at the Hub.
Hand begins making security checks of all the agents but her men inform her that Triplett and Simmons are unaccounted for. They covertly send out a transmission to Agent Weaver, who is frantically telling them to save themselves because HYDRA is taking over. She tells Jemma not to trust anyone just as the transmission ends. Triplett locks the door and a scared Simmons begins to fear him. As he comes closer he draws a knife, but he turns it over to her to prove his trustworthiness.
May awakens in handcuffs in the containment room, and Ward demands an explanation. She calls him out on letting his emotions control him during their last mission. Coulson barges in to tell her that Fitz repaired the direct line to Fury. She dials for the director as Garrett explains to Ward that Agent Hand is the clairvoyant. Instead of getting through to Nick Fury, however, May hears a man's voice saying that he is dead. HYDRA agents begin shooting at the plane.
After Coulson removes May's tracker from her arm, he asks for an explanation. He realizes that she knew about the events of TAHITI. She reveals that she was the one who actually assembled Coulson's team. The whole time, she was trying to protect him by monitoring any side effects of the drugs used to save him. She tells him that she is in no way affiliated in the current HYDRA threat. Ward tells them that currently there are no HYDRA agents outside and they should sieze the chance to leave with whatever they can manage.
They wipe the memory of the computers on the bus and move it to a flash drive, including information on the 0-8-4, the Asgardian berzerker staff, and Donny's weather machine. As HYDRA agents infiltrate the Bus, they do not find the agents who have already escaped.
Agents break into the lab where Simmons and Triplett are hiding, ordering for them to put their hands up. The agents split up: Ward and Skye go to disable the systems. Garrett, Coulson, Fitz, and a handcuffed May go to extract Simmons.
Agent Hand gives her captives the choice to swear allegiance to HYDRA or to share in Fury's fate. Triplett uses his fighting abilities to wrestle a man's gun away and to hold it at his head. Hand reveals this is the correct answer as she is really on S.H.I.E.L.D.'s side still. She tells Simmons that only Coulson is actually on Coulson's side.
At a surveillance room, May and Coulson in supposed custody are ushered in by Garrett but the agents proceed to take down the security team with ICERs.
After Coulson is not found on the plane, Hand agrees that they should have blown his plane out of the sky. Simmons says she can't kill Coulson, but Agent Hand still maintains that Coulson is guilty because "the lies add up".
Grant and Skye emerge in a janitor's closet. He wants to clear the way for Skye to the control room. He tells her the reason he killed the decoy clairvoyant was because he was trying to protect her. He takes her ICER and says that if they "make it out of this" they could get a drink. He mentions the bar in Dublin and says he wants to take her up on the offer to talk. She agrees and the two kiss, before he emerges to fight the opposing agents. He takes out most of the men but the battle shifts against his favor as he is pinned on the ground. As Skye listens on, she fears for him, but he is the victor. Instead of hacking the system, Skye plans on blowing it up.
As Agent Hand draws closer, Garrett still determines to kill Hand. He claims he wants revenge for the three agents he lost, but Coulson questions his motives. Soon, after Garrett reveals information that he would not possibly know, Coulson realizes the truth: Garrett is the clairvoyant. He also realizes that he "led the clairvoyant to the cure" as said by Ian Quinn. As Hand's agents come in to take down Coulson and the other agents, Coulson informs them that they should take Garrett. The traitor talks to the group of agents, which is revealed to be partly comprised of HYDRA agents on Garrett's side. With a "Hail HYDRA", Garrett lines up Coulson, May, and Fitz.
Garrett attempts to persuade the agents to join him with HYDRA, but the three stay loyal to S.H.I.E.L.D. Just before Garrett's men open fire on them, the explosion caused by Skye distracts the HYDRA agents long enough for May and Coulson to jump to action. Initially Fitz hides, but he shoots an agent about to take out May. Fitz tosses Coulson a soundwave repulsor, just before Garrett can stab Phil. After the weapon is deployed, Garrett is thrown against the wall and is knocked out. Victoria Hand and her team of loyal S.H.I.E.L.D. agents apprehend the agents that are working for HYDRA, including Garrett.
Agent Hand tells Coulson the status of S.H.I.E.L.D. worldwide and mentions that things are bleak. Ward asks for permission to accompany Hand to the fridge to take Garrett. All the agents are somewhat depressed that the Bus is in shambles, but Coulson gives orders to fly somewhere to survive.
On the way to taking Garrett to the prison, Hand asks Ward if he would care to shoot the true clairvoyant since he failed the first time. Grant cocks his gun and prepares to shoot, but instead he takes out the two S.H.I.E.L.D. agents and Victoria Hand and allows Garrett to go free.
In the cockpit, Garrett is now back to his normal self, but Ward is visibly shaken and angry by what happened.