Nighttime in Washington DC, and former S.H.I.E.L.D. agent Maria Hill leaves the Department of Justice. She calls an associate and tells them that Congress is questioning her about her involvement in S.H.I.E.L.D., now considered a terrorist organization after HYDRA's infiltration. Maria spots several FBI agents following her, but then realizes that someone has knocked them out. She ducks into an alley, gun drawn, and finds Melinda waiting for her. Melinda admits that she knocked out the agents and asks Maria, who is now working in the private sector, to help Coulson. When Maria wonders why, Melinda tells her that Coulson doesn't trust her anymore. Maria asks what Coulson knows about TAHITI, and Melinda asks her if HYDRA infiltrator Alexander Pierce was the one who had Fury resurrect Coulson... and possibly reprogram Coulson's mind. The former agent admits that she doesn't know because Fury buried the intel, and insists that Fury is dead. The police arrive to investigate the downed agents and Maria drops her gun while Melinda slips off into the shadows.
At Providence, Fitz and the others watch the security footage of first Melinda leaving the base alone, and then Grant and Skye boarding the Bus hand-in-hand and flying off. The rest of the footage is wiped and there's no indication of what happened to the missing Agent Koenig. Coulson admits that he told Melinda to leave, and Trip angrily says that they're better off without her if she couldn't handle it. As Coulson glares at him, Jemma goes to get some food, Fitz goes with her and she figures that something will turn up. She decides to make pancakes and asks Fitz to warm up the griddle while she gets some pancake mix from storage. As Fitz heads down the hallway, he glances into Koenig's office and notices that one of the fake windows is showing a nighttime scene and the other is showing a daytime scene.
Coulson figures that Koenig learned about something that they need to know.
Fitz examines the nighttime window and discovers a pen jammed in it.
As Jemma leaves the storage room with the pancake mix, she notices blood on the door.
Coulson tells Trip that Koenig learned that they had a traitor.
Fitz removes the pen and the screen rises, revealing a message that Skye wrote: "Ward is HYDRA." In the distance, Jemma screams.
On the Bus, Skye watches as Grant spray-paints over the S.H.I.E.L.D. logo, and starts looking for a sat phone. Grant notices and comes over to tell her that he already called Coulson and the team is fine at Providence. He asks why she picked a diner in LA as the GPS coordinates to decrypt the hard drive, and Skye reminds him that it was where she met Mike Peterson and got involved with S.H.I.E.L.D. for the first time. Grant notices that she has a gun in her belt and gently takes it from her, assuring Skye that she'll be safe with him and they can't afford the police arresting her on a concealed-weapons charge. He tell Skye that he's going to watch her at all times to make sure that she's safe.
Jemma performs an autopsy on Koenig while Fitz paces nervously back and forth. Trip tells him to calm down and Fitz snaps at him, pointing out that they still don't know much about him. The scientist insists that Grant can't be the traitor and that HYDRA is trying to frame his friend to throw them off the scent. Jemma confirms that Koenig was garroted and that the killer was Grant's height, and strong enough to lift Koenig up into the drop space. Furious Fitz starts smashing things off of tables until Coulson grabs him and says that he has to focus his anger into saving Skye. He reminds them that Skye knows that Grant is a killer and that she's with him now, and that they need to repair the broken communications links so they can locate the bus.
As Grant and Skye walk to the diner, he demands to know how long it will take to decrypt the hard time. Skye claims that because she only has her laptop to work with, it will take at least an hour.
While Fitz repairs the communication lines, Coulson and Trip hook up the computer. As they work, Coulson figures that Garrett is alive and Hand is dead, and that HYDRA has all the weapons from the Fridge that they need. The two men realize that Grant is keeping Skye alive because HYDRA wants the information on the hard drive, and Skye must have encoded it. When they hook up the computer, they get a ping on the Bus in Los Angeles. The intruder alert goes off and the two agents confirm there are multiple targets closing in on the base.
After they sit down at the diner, Skye complains that Grant keeps staring at her. He apologizes for stressing her out but insists on sitting across from her. Skye brings up her laptop and Grant realizes that she's hiding something. She says that she was thinking of Mike and how things have changed: he's a killer and they're on the FBI's most wanted list. As Grant tells Skye that she's doing great, two policemen come in.
At Providence, Coulson and the others prepare to repel the invaders. Coulson assures his teammates that no one could get through the door, just as it open. The intruders are U.S. Special Forces and Colonel Talbot is with them. He calls on the team to come out, and Coulson steps out after confirming they won't shoot. When Coulson wonders how they go tin, Maria walks in and says that she told Talbot the access codes.
An old man is visiting a cemetery when he hears someone digging nearby. He walks over and finds Melinda digging up a coffin at Coulson's gravesite. She removes a small canister from the coffin and offers the man her condolences, and then goes back to her car. When Melinda opens the canister, she finds a flash drive inside and plugs it into her laptop, and confirms that it has a final report on the TAHITI project to Fury from the project director.
Coulson and his people surrender to Talbot, who talks to Jemma, Fitz, and Trip in the mess hall. Talbot reminds them that most of the world thinks that S.H.I.E.L.D. is a terrorist organization, but that if they give him actionable intelligence then he can insure them time served for cooperating. Jemma insists that Talbot should focus on the rogue HYDRA agent but the colonel isn't interested and warns them that S.H.I.E.L.D. high command has gone to the private sector. That leaves agents like the team in Talbot's hands, to do with as he wishes.
Maria takes Coulson to the base office and tries to convince him to make a deal. If he helps her turn Providence over to Talbot and his superiors, she can get him released. However, Maria admits that the others will have to go through processing. Coulson refuse and figures that Maria considers him a liability. She points out that he is and Coulson tells her to worry about the HYDRA double-agent, not him. He explains that Grant is the traitor and Garrett is still alive, and insists that they have to rescue Skye. Talbot and his men come in and ask if they're going to comply. Maria and Coulson attack them instead and Coulson finally grabs an Icer from the desk drawer and stuns the Special Forces men.
At the diner, Skye continues stalling for time, while Grant checks out the policemen who are at the counter. She suggests that he pretend to be an impatient boyfriend and then asks him about his previous undercover assignments and how hard it must be to live a double-life. Grant grows increasingly uncomfortable but Skye continues, asking him what he would have said to Garrett if he had a chance to talk to him before he shot him. She calls Garrett a lousy traitor and Grant wonders what she's up to, and Skye tells him that she's trying to have an honest conversation with him for once.
The police start escorting people out and Grant says that they should go, figuring that they've been made. Skye refuses to go with him, and shows him her computer screen... with a "wanted fugitive" photo of Grant. She tells Grant that she tipped off the police just as the officers order them both to surrender. Grant attacks them while Skye grab her laptop and runs outside. Two policemen arrive and Skye begs them to arrest her, saying that she's a S.H.I.E.L.D. agent and wanted by the authorities. They finally subdue her, but Grant comes out and kneecaps them. Skye drives off in the police car, but Deathlok is standing in the road ahead. The cyborg leaps onto the hood of the police cruiser, smashes his arm through the windshield, and grabs Skye.
The two HYDRA operatives take Skye back to the Bus and Deathlok tells Grant that Garrett sent him as backup because he figured Grant was weak on Skye. When Grant insists that he can handle Skye, she speaks up and points out that he hasn't been able to handle her so far. Grant tells Deathlok to give them five minutes and turns to Skye, who attacks him. He warns her that she can't win, but she head-butts him so he handcuffs her to the staircase railing. Grant assures her that what he did to her wasn't personal, insisting that he was a spy and he had a job. Skye doesn't buy it asks if he's going to kill her since HYDRA had her shot once before. Grant insists that Garrett was the one who had Quinn shoot her, and that he couldn't do it because of his feelings for her. Skye doesn't believe her but Grant insists that his feelings for her have always been real. Furious, he says that he's a survivor and that he made tough decisions to stay alive, and one day she'll understand. Disgusted, Skye tells him that she'll never give him what he wants.
In the main lounge, Deathlok tries and fails to access the hard drive. Garrett sends him a message via his optical implant that he's done waiting and Deathlok should go to Plan B. Deathlok goes back to the lab and tells Skye that her time is up. She tries to get through to the man he was, reminding him that he has a son. However, Deathlok says that nobody can protect his son Ace now that S.H.I.E.L.D. has been torn apart, and that HYDRA has implanted an explosive implant in his brain that they can detonate if he disobeys their orders.
Skye insists that Deathlok has some good in him, and that Quinn had to shoot her in Italy because Deathlok couldn't. Deathlok admits that he's not going to hurt her... and then shoots an electrical device into Grant's chest, stopping his heart. Deathlok says that he will only start Grant's heart back up if Skye decrypts the hard drive. She refuses, saying that she hates Grant, but Deathlok asks if she hates him enough to become a murderer. As Grant lies on the floor gasping his last breaths, Skye finally breaks and tells Deathlok that the hard drive is decrypted by altitude. Deathlok restarts Grant's heart and tells Skye to enter the password so the drive will decrypt automatically when they reach the proper altitude. The cyborg then tells Gran to get the Bus in the air.
As Grant prepares to lift off, Maria and Trip arrive in another plane and Maria orders Grant to stand down. He refuses, figuring that Coulson won't let anyone open fire on them as long as he has Skye. Maria tells Grant that he doesn't owe Garrett anything, but Grant says that she's wrong and lifts off. Trip wonders if they should track the Bus, but Maria tells him that they bought Coulson enough time.
Coulson has already entered the Bus via the wheel well and goes to the interrogation cell. He frees Skye and leads her through the lounge to the counterpart, and she asks if he's already dealt with Deathlok. Coulson wasn't aware that Deathlok was aboard... just as the cyborg steps forward. Coulson and Skye run for the cargo bay and Coiuilson opens the cargo ramp, and Grant sees the warning on his board. He heads back with Deathlok and opens fire, and Coulson activates the machineguns on his car, Lola, and opens fire on Deathlok. Once Skye is in the car, Coulson gets in and backs it off the ramp. The car plummets toward the earth and Coulson just manages to grab Skye before she falls out. He manages to get the flight mechanism activated just in time and they come to a landing at a stadium. The parking attendant comes over and asks them to pay the fee.
On the Bus, Grant wants to go after them but Deathlok tells him that they have to deliver the hard drive to Garrett. Before he goes back to the cockpit, Grant tells Deathlok that he'll kill him if he does that again, and Deathlok assures him that it was nothing personal.
Coulson and Skye meet Maria and the team at a motel and he talks to Maria. She warns him that there is no S.H.I.E.L.D. anymore and no backup, and advises him to let his people go their separate ways once he finishes off Garrett and Grant. She suggests that he get a job with Tony Stark but Coulson says that's not his and Maria leaves.
Fitz and Jemma are out at the pool and Fitz wonders why Grant did it. When Jemma says that some people are just evil, Fitz asks if she's working for HDYRA. She wonders why he's asking and Fitz says that he needs to hear it from her. Jemma tells him that she's not a HYDRA double-agent and Fitz says that he isn't either. He tells her that if she was, then he wouldn't know what he would do. Jemma assures him that he'll never have to find out and puts one hand reassuringly on his knee.
Nearby, Skye and Trip are relaxing and Coulson comes out to tell to take a break for the night. Trip goes to get some junk food and Coulson buys two candy bars from a vending machine. He gives one of them to Skye and eats the other himself, and assures her that they'll get Grant. Skye tells her boss that she left a little surprise for HYDRA on the hard drive, and the two of them sit back and look up at the sky.
Later when Coulson returns to his room, he finds Melinda waiting for him. She knows about Grant from Maria, and plays the final report that she found in Coulson's grave. On it, Coulson is telling Fury that he's resigning from the TAHITI project because the testing is too dangerous. The side effects of the TAHITI project cause psychosis and catatonia because of the trauma of their resurrection. The only solution that the scientists can come up with is induced amnesia and then the addition of new memories, but even then the results are inconsistent at best.