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In Washington D.C., Maria Hill is talking on her cell phone about her recent questionings with Congress about the Fridge and its occupants (including Man-Thing). She realizes that they are keeping a surveillance team on her to follow her. The three undercovers are taken out and Hill cautiously goes into an alley where Melinda May is waiting for her. She tells Hill that Coulson needs help. Even Maria Hill is unaware of who was overseeing Coulson's operation at T.A.H.I.T.I. She says that the only thing Director Fury said was that he "buried that intel, when he decided not to bury Coulson." The police drive up to take Maria Hill into custody, as May vanishes.
At Providence, Coulson asks Fitz to replay the security footage another time. All they have is May leaving the Bus with her things and soon leaving the base, and, not long after, Ward and Skye enter and take off in the plane. They find no sign of Koenig leaving the base and no explanation to the communications being cut. Fitz and Simmons leave the viewing room to get snacks.
As Fitz goes down one hallway, he notices a suspicious sign visible inside the bathroom. At the same time, Jemma enters the supply closet. Triplett and Coulson discuss the peculiarities. The worse case scenario is that they have "had a wolf in the herd the whole time". Fitz discovers a secret message saying "Ward is HYDRA", just as Simmons screams after finding Koenig's corpse above the supply closet.
In the Bus, Ward spray paints over the S.H.I.E.L.D. emblems on the side of their van, while Skye works with the flashdrive. Skye searches for the satellite phone to contact the team, but Ward claims to have already corresponded with Coulson. Their plane is headed to the diner where Skye first met Mike Peterson. Ward hugs her but takes her concealed gun away to avoid looking suspicious.
Simmons examines Koenig's dead body and discovers that the build of the killer was matching that of Ward. Fitz angrily throws things because he doubts Ward is against them. Coulson motivates Fitz to track their plane.
The couple walk into the diner, but Grant is impatient because it will take a while for Skye to decode her flashdrive.
Triplett begins working to bring communications back online. Coulson realizes that Garrett is still alive and that HYDRA has valuable weapons from the Fridge at their disposal. They also realize that Skye is the reason Ward came back. Just as they find the location of the Bus, squadrons of non-S.H.I.E.L.D. forces move closer to their current location.
As Skye attempts to hack, Ward goes extremely more impatient. Her computer reveals that her location is invalid for the encryption. Ward notices her worry, but distracts him by telling of her experience with Mike Peterson. Ward becomes uneasy when police officers enter.
At Providence, Coulson prepares against a HYDRA attack, but it's revealed to be led by Glenn Talbot and special forces. When Coulson asks of how they found the top secret base, Talbot reveals that he did not come alone and Agent Hill tells him that she led Talbot there.
In a graveyard, Agent May climbs out of an empty grave she had dug up, with a small metal canister. The name on the tombstone is shown to be "Phillip Coulson" and the casket is empty. In her car she finds that the canister conceals a USB which when plugged into her computer, has files for the final report of the T.A.H.I.T.I. project. She plays the file and is surprised.
Talbot interrogates the agents, trying to convince them to turn themselves in. Maria Hill tries to convince Coulson to give Providence to the military. He angrily confronts her about keeping secrets about the procedure and tells her that Ward is no longer on S.H.I.E.L.D.'s side. When Talbot enters with two men, Coulson and Hill take them down and knock them out with a night-night pistol. They quickly begin leaving Providence.
In the diner, Ward is anxious because more police cars start pulling up. She asks about Ward's longest undercover experience. She soon reveals that the cops are preparing to take Grant in because she turned him in. As officers move in, Ward fights them, but Skye tries to flee. She tries to get herself arrested but Skye shoots the two arresting officers. She takes off in their police vehicle where Deathlok stops her.
Back in the Bus, Ward and Mike verbally fight, but Skye tells them that she will not tell them the secret to unlock the flashdrive. Skye hits Grant several times until he handcuffs her to a metal rail. She confronts him on his lying, but he claims his feelings for her are real. He says that she will understand someday.
In the mission room, still in shambles, Deathlok tries to decode the flashdrive himself. In his eye, Mike is ordered by the clairvoyant to move to plan B. He interrogates her about unlocking the drive. Because she refuses to tell, he places an electric device on Ward's chest to stop his heart. He says he will restart Ward's functions if she agrees to tell. Because she is a good person, she does not want to see Ward suffer. She reveals that the location lock on the flashdrive is based on altitude location. Deathlok tells Ward to start the plane.
Two planes, one piloted by Ward and the other by Hill, sit across from each other on a runway. She attempts to stop him from leaving, but after an exchange of words, he lifts off. Though Ward thinks he is getting away, it is revealed that Coulson boarded the Bus on the landing gear.
Coulson climbs into the main area of the Bus and discovers Skye in the interrogation room. She regretfully tells him that she unlocked the drive. He is not worried because he is about to take down Ward, but Skye reveals that Deathlok is on the plane, something Coulson never accounted for. Ward and Mike go after Coulson and Skye, who quickly jump into Lola to fly back down to the earth's surface.
Mike Peterson refuses to land the plane because he does not want to deviate from the plan again.
The agents unwind at a motel before their next mission. Maria Hill tells Coulson that he should stop chasing Garrett and Ward, because there are no more safe places for the S.H.I.E.L.D. agents. Sitting by the pool, Fitz insists that he has to hear Simmons say she is not HYDRA. He says he would not know what to do if she were but she tells him that he will never have to find out. Coulson assures Skye that they'll find Ward. She says that she left Grant and Deathlok "a little present" when she unlocked the flashdrive.
When he enters his hotel room, Coulson finds May waiting for him. He is glad she returned. She shows him the information on the USB she found earlier. She plays the video file for him: it is a video of Coulson telling Director Fury that he will resign from his job on the T.A.H.I.T.I. project due to its extreme results. At first the subjects of the program were well, regenerating as planned, but soon a mental breakdown occurred. He says that memory replacement is the only way to protect these "subjects" and that the T.A.H.I.T.I. should be terminated.