In her cell, Raina is making an origami flower and puts it on the shelf with the others she's made. There are explosions and gunfire outside, and Raina sits calmly on her bunk. Ward comes in and she backs away nervously, and the agent hands her a gift-wrapped box and says that it's a gift from the Clairvoyant. Raina opens it and finds a flowered dress inside.
At the Hub, Coulson is watching a newscast about how S.H.I.E.L.D. has been crippled. Skye tells him that there are three secure S.H.I.E.L.D. bases, including the Hub, and admits that Coulson was right about how there's no one left to protect the world. Coulson assures her that they made it through and they'll protect the world against HYDRA, and they can fight them since their team is intact.
Ward takes Raina to a barbershop in Havana. Raina wonders if that's where they're meeting the Clairvoyant, and Garrett turns around in the barber chair and tells her that there's no reason to call him that anymore. He introduces himself and Raina says that it's an honor to meet him. Garrett thanks her for her work on the Centipede project, and tells her that he obtained all of his information from his S.H.I.E.L.D. security clearance. Raina is shocked to learn that he isn't clairvoyant and accuses him of being a fraud, and Garrett admits that he had to do it to change the world. He invites Raina to take a seat so he can show her how he plans to do it. Raina hesitantly sits in the barber chair and Garrett welcomes her to HYDRA... and the chair descends into the floor.
Fitzsimmons are coordinating repair teams working on the Bus, and Jemma points out that they have no jurisdiction now that S.H.I.E.L.D. has been labeled a terrorist organization. Fitz figures that it will all work out. Triplett is helping them and shorts out the wiring, and Fitz angrily walks off.
In the control center, Skye tells Coulson that they've retaken the Cube and now have four secure bases. Melinda comes in and tells them that the Bus is back on line. Colonel Glen Talbot of the USAF calls in and demands to speak to Coulson. Coulson says that S.H.I.E.L.D. is ready to aid him, but Talbot says that he's sending a peacekeeping force in to take control. Once Talbot signs off, Coulson figures that Talbot is lying. He'll probably subpoena them all and tie them up in court at best, or launch an assault at worse. He tells Skye to enact Odyssey Protocol so that Fitz finishes the repairs so they can leave.
At the Bus, Melinda tells Coulson that most of the agents are staying behind to surrender. The Bus' fuel reserves are tapped out but Melinda assures Coulson that they'll be up in 10. Triplett offers to join them now that they're short Ward. Coulson refuses, suspecting that he was working with Garrett, but Triplett insists that his SO had him fooled and got three of his friends killed. Jemma speaks up, pointing out that Triplett was willing to die in defense of S.H.I.E.L.D.. Coulson agrees but tells Jemma that Triplett is her responsibility.
The Bus takes off and Coulson tells Fitz that they need to stay off the radar. Fitz says that they have to stay in the air as long as possible rather than risk landing. Jemma warns that they're low on food, and Triplett informs Coulson that a fuel line is leaking. Skye reports that they have Internet and Coulson puts her to work wiping their records so that no one can prove they exist. When Skye warns that it's a desperation option and can't be undone, Coulson points out that it's their only option when the world governments start hunting them. As he turns to go, Skye asks if he's heard from Ward. He admits that he hasn't and gives Skye a cell phone to call Ward with.
Coulson goes to the cockpit and Melinda confirms that she hasn't spotted Talbot's forces yet. Due to the fuel line, they only have four hours in the air and Melinda asks where they're going. Coulson admits that he doesn't know and walks out.
While Skye wipes the team's records, she calls Ward. Garrett tells Ward to take it and Skye tells him what's going on. Ward claims that Hand is taking the long route to the Fridge and asks where Coulson is headed. Skye says that she'll keep him posted and tells him to be careful. Once Ward hangs up, Garrett admits that he's impressed that Ward managed to blend into his role so long. Ward isn't happy that they shot Skye as part of the operation, and Garrett says that he should have contacted him if he had a thing for Skye. He points out that Skye was onto Centipede long before she joined S.H.I.E.L.D. and figures that eliminating her was the safe bet. Ward reminds him that Garrett didn't want bloodshed and Garrett points out that was only until they discovered that Coulson knew nothing. He reminds Ward that he was the one who gave him his assignment and assures him that they're closer than ever to getting what they want.
Garrett and Ward go to Raina, who is examining the Centipede equipment. He tells her that she's to continue with Phase 3 and that they've developed several new drugs based on the samples they took from the Guest House. Garrett admits that it was destroyed and none of the drugs have been working as planned. He tells Raina that he can't succeed without her help, and assures her that she has all the money she needs. Ward gives Raina the hard drive with all of the team's information on it, including Jemma's research on the Guest House drug. Garrett and Ward then head out to raid the Fridge now that it's vulnerable.
Melinda takes the Bus low over the ocean to avoid radar. Skye collects the team's badges and gives them to Coulson, and admits that she's disappointed that it's worthless. Coulson adds his own badge to the pile and Skye realizes that he gave his life to S.H.I.E.L.D.. He talks about how Fury recruited him out of high school and that sometimes it feels like forever. As Coulson locks up the badges in the safe, Skye notices that his badge is glowing. A set of coordinates have appeared on it and Coulson figures that Fury sent them.
Coulson tells the rest of the team that Fury is alive, while Skye confirms that the coordinates are for somewhere in the Canadian wilderness. Triplett suspects that it's a trap but Coulson says that Fury gave him the badge and he swore to be a shield for the world. He's sure that Fury sent the coordinates and invites anyone who doesn't believe that to parachute out.
Garrett meets with his assault team, while Raina tells Ward that if Garrett really had clairvoyant powers, there was a question she had for him. She asks Ward about Garrett, and Ward explains that Garrett saved him from himself when he was a teenager. Ward wonders if Raina is trying to work him, and she said that if she wanted to work him then she'd ask about Coulson and the team. She's surprised that Melinda didn't suspect anything, and Ward explains that he became intimate with her to keep his distracted. As for getting close to Coulson, he gave him someone he thought he could help. Raina wonders if Ward feels he owes Coulson something, and Ward admits that he does... but says that he owes Garrett everything.
Melinda comes to see Coulson and confiscate his weapon. She figures that Fury is dead and HYDRA is manipulating Coulson's brain. Coulson points out that Fury ordered the surgery, but Melinda says that someone else was behind it. Shocked, Coulson asks who it was and Melinda admits that Fury is the only one who knows. She is worried that HYDRA is controlling Coulson's actions, but Coulson refuses to hand over his weapon and dares her to try and take it. Melinda doesn't and Coulson orders her out of his office.
As they check supplies, Triplett tells Jemma and Fitz that Coulson is obsessed. Fitz doesn't believe it, but Jemma agrees with Triplett. Disgusted, Fitz says that now's the time when they stick with the man they believe in.
At the Fridge, Garrett and Ward land on the roof and Ward pretends to have Garrett prisoner. The guards refuse to let them in without Hand present, but Ward points out that she's busy. When Ward threatens to radio her, they tell him to do it. A helicopter flies up and opens fire, and the guards figure that it's HYDRA. When the helicopter comes back for another pass, one of the guards finally lets Ward and Garrett in. They all retreat into the elevator and Ward shoots the two men dead.
Garrett and Ward descend through the building, using gas to knock out the security forces. Once the gas clears, Garrett opens the vault containing the confiscated equipment that S.H.I.E.L.D. supposedly launched into space. He tells his men to grab everything and finds the plasma weapon the team recovered in Peru.
Melinda lands the Bus seven miles from the coordinates. Triplett suggests that he and Melinda check it out first, but Coulson says that they only have eight hours until a NATO satellite passes overhead and spots them. He tells the team that each of them have to choose whether they're going to go or not, but he's going no matter what. Coulson heads out and after a moment, the others follow.
A the Fridge, Ward recovers the Asgard staff while Garrett uses the weapon to free all of the super-human prisoners S.H.I.E.L.D. has been keeping. Ward paces off a specific distance and takes the weapon from Garrett, and blasts a hole in the floor, revealing a glowing object below.
The team makes its way through the wilderness. Fitz scans the area and doesn't detect anything, and Jemma asks him if he believes what he said earlier about trusting Coulson. When Fitz admits that he isn't sure, Jemma says that at least they have each other. Fitz says that he doesn't want things to change but Jemma tells him that it's too late for that.
As they follow Coulson, Skye asks Melinda if Coulson is okay and asks why Fury had her spy on Coulson. Melinda finally says that Fury was worried that Coulson finding the truth would have negative consequences. When Skye points out that Coulson's whole world has fallen apart, Melinda notes that he's not the only one.
Coulson reaches the coordinates but there's nothing visible. When Skye wonders how long they should search before going back, Coulson says that they're not going back and that the Bus is out of fuel in any case. The others wonder if he knew that before he flew them out there, and Coulson desperately insists that there has to be something there. He tells the team that they can't let HYDRA define them, and then apologizes. Coulson throws the badge into the air and an automated machinegun pops up and shoots it.
The team take cover as the machinegun swings around. Coulson figures that it's Fury reaching out, and steps out to prove his theory. The gun aims at him and a man asks him over an intercom for identification. When Coulson identifies himself, a hidden door opens in the nearby rock face.
Back at the HYDRA base, Raina tells Garrett and Ward that there's a complication with the hard drive. Skye programmed it to erase all data if anyone but Skye accesses it. Garrett tells Ward that he knows what it means.
Coulson and the others enter the underground base and a S.H.I.E.L.D. agent, Eric Koenig, steps out and explains that he calls it Providence, one of Fury's secret bases. Koenig leads them to a mess hall and explains that he's a level 6 agent. Coulson wonders what happened to Fury, and Koenig says that the director didn't make it out of DC and the Fridge has fallen. Skye calls Ward while Koenig asks to speak to Coulson privately.
Once Coulson is alone with Koenig in the command office, Koenig explains that he's been there since the Chitauri invasion. He then tells Coulson that Fury is alive and he's under orders not to tell the rest of the team. However, he has no idea where Fury is. Koenig insists that no one else can know and asks Coulson if they're good. Coulson says that they are and Koenig says that they need to have Melinda pull the Bus in.
Once Ward signs off, he tells Garrett the news about the secret base and that Fury is dead. As Garrett dresses, covering over a metal plate in his chest, he admits to Ward that they all have their weaknesses. He assures Ward that he'll have 24 hours alone with Skye to get the information, because they plan on keeping Coulson distracted. If Ward can't get it done, he's to kill the team and bring Skye in. Garrett then beats Ward to make his story believable.
Later, Ward makes his way to the base and identifies himself. The door opens and Skye is there to greet him. She says that Jemma should take a look at his injuries and then they can have that drink they discussed.
At the HYDRA base, Raina brings Ian Quinn in. Quinn is less than thrilled that he was locked up because of Garrett, and he's been beaten and had his assets frozen. Raina has told him how Garrett was only pretending to be clairvoyant, and Quinn refuses to work for Garrett any further. Garrett tells Quinn that he has a special gift just for him and leads him to an adjoining chamber. Inside is the gravitonium sphere, and Quinn thanks Garrett.