Coulson is captured and taken to an underground base in Siberia. The soldiers take him to a room and handcuff him to a chair, but he seems remarkably unconcerned. The interrogator comes in and Coulson calls him Shaw, asking if he has the intel on him. As the soldiers look on, puzzled, Coulson tells Shaw that "they" know and the two of them have three minutes. Shaw attacks the soldiers and Grant and Melinda break in and take them on as well. Melinda cuts Coulson free and they head down a tunnel to a surface hatch. A sled is waiting for them, tied to the transport plane, and it tows them away across the snow.
Later in the lab, Jemma removes the memory device from Shaw's sinus cavity using a probe. Coulson, looking on, tells Shaw that they're headed for The Hub to drop it off and will drop him off as well. Jemma and Coulson go out to the lodge and Skye wonders what's going on. Coulson tells her that the mission and the intel is Level 8 Classified and refuses to discuss it further. When Skye asks why they can't discuss it, Grant and Melinda tell her that S.H.I.E.L.D. relies on compartmentalization to keep important information from falling into enemy hands. Melinda warns the hacker that Coulson handles things a bit differently than The Hub does.
When the team arrive at The Hub, Coulson informs Skye that she doesn't receive an access badge. Agent Sitwell arrives to greet them and then escorts Coulson, Grant, and Melinda, to Agent Victoria Hand, the person in charge. Victoria explains that the intel concerns an overkill device: a sonic weapon that can set off and destroy all forms of weaponry. Terrorists are building the device at their compound in South Ossetia and plan to extort Russia into giving their country independence. Victoria needs two agents to cross the disputed border, enter the compound, and disable the overkill device. Grant points out that he has experience in the area, and Victoria tells them that they don't have specs on the device so they'll need to send in a tech expert.
Fitz is collecting some equipment on a cart and trying to get through an automatic door without much luck. Coulson, Grant, and Melinda arrive and watch, and Grant wonders if they're really taking the scientist along. They head back to the plane and brief Fitz on the mission. Jemma worries about whether he can handle it, and Fitz tells her that he has it under control. His friend gives him a scientist to take on the mission and Skye gives him his mag pouch full of specialized equipment.
In the conference room, Coulson reviews the mission specs with Melinda and Grant. She notes that they have to disable the overkill device by 0600 hours and then wait for a S.H.I.E.L.D. exfil team to get them out. Coulson tells Grant to take care of Fitz, just as Fitz arrives. As the others leave, Skye hangs back and asks Coulson if the mission feels right to him. He tells her that the operations people who planned the mission are the best at what they do.
Later, Grant and Fitz drive to a bar in the Caucasus Mountains where Uri Dubrovsky, Grant's contact in the area, does his drinking. They go in and Grant orders a drink for himself and another for Uri. A big Russian, Vladimi, walks over and tells him that Uri dead. The customers draw their guns and Vladimi tells Grant that he has no friends in the bar.
On the plane, Jemma worries about Fitz and Skye suggests that they talk to Melinda, who has a higher classification and may know something useful. Melinda refuses to discuss it except to say that they'll wait and react at the proper time. Less than satisfied, Skye tells Jemma that she's going to go to Coulson for some answers.
In the S.H.I.E.L.D. operations room, Coulson and Victoria are watching the area through satellite surveillance. Victoria half-jokingly notes that Fury has a soft spot for his favorites and that Coulson is one of them. She mentions his recovery in Tahiti and Coulson starts to repeat "It's a magical place," but then catches himself. He tells Victoria that his people can handle themselves in the field.
Vladimi and the others tie Grant and Fitz up and dump them in a backroom. When Fitz wonders why the Russians are waiting, Grant explains that they're waiting for their boss to arrive. The boss, Marta, soon comes in and Grant explains that they're there to stop the separatists. He asks for her help getting across the border, but Marta refuses, noting she has no reason to trust them. As Vladimi prepares to shoot them, all of the lights go out.
Skye finds Coulson and asks about the mission, noting that The Hub is on high alert. He simply tells her to trust the system and walks off. When Jemma arrives, Skye tells her that they'll have to do some digging and Jemma realizes that she's planning a hack. Skye tells her friend that they have to do what they can for Grant and Fitz, and Jemma reluctantly asks what she has in mind.
Fitz offers to repair the bar's generator and soon has it working. Marta gets him a drink and he start negotiating their trip over the border. Grant and Fitz are soon in Marta's delivery truck heading for the border. Fitz tells his teammate that he used a personal EMP device to short out the generator so that he could fix it and win Marta's trust. The truck stops at the border and they hear soldiers approaching. Grant kicks out a beer keg and shoots it, causing a diversion. He takes out the first few men but more are on the way and the two men are forced to run.
Coulson goes back to the plane to talk about his concerns with Melinda. She's busy performing a kata and tries to ignore him. Despite his worries about keeping secrets from the team, Coulson convinces himself to trust the system and walks off.
Skye gives Jemma a flash drive and explains that if the scientist can get it into the system then the hacker can access the system for four minutes. Jemma goes into The Hub's computer core and gets the access panel open... just as Agent Sitwell arrives.
Grant and Fitz take refuge in a drain pipe and hide from the patrols. Fitz worries that they may not be able to stop the separatists in time.
Sitwell wonders what Jemma is doing in the computer room, and Skye tells Jemma over the comm to distract the agent. Jemma tries to flirt but Sitwell realizes that she's violating base security. As he tries to call security, Jemma shoots him with the night-night gun and plugs in the flash drive, then hides Sitwell. She get out and Skye suggests that they go to Melinda for help.
As they wait, Fitz wonders why S.H.I.E.L.D. only sent in two agents. He offers Grant half of his sandwich and the field agent immediately throws it in the water. He explains that the soldiers are using dogs to track them and they can smell the sandwich. Fitz irritably congratulates Grant on rescuing him from a sandwich, and Grant says that Coulson asked him to protect his teammate.
Skye hacks the S.H.I.E.L.D. computers and finally locates a file showing S.H.I.E.L.D. troops all around the compound. However, there's no indication of an exfil team. Coulson comes in and closes her laptop, telling her that she should trust the system. Skye angrily tells him that S.H.I.E.L.D. has sent their friends on a suicide mission.
The sun comes and Grant and Fitz lie in the middle of a road and bicker about the sandwich. When they hear a truck approaching, they cover themselves with a high-tech chameleon tarp, let the truck pass over them, and grab the bottom.
Coulson argues with Skye about her breech of security, insisting that S.H.I.E.L.D. is keeping secrets for their own good. Skye doesn't believe it and insists that she had to go off-book to save their friends. Coulson tells her that the book exists for a reason, and he needs to know if he can trust her to keep a secret if he gives her one. As he heads off, Skye asks Coulson if he knew about the plan. Coulson hesitates and then tells her that's classified.
At the compound, Grant and Fitz find a door leading inside. While Grant signals for extraction, Fitz uses an x-ray device to spot the guards inside. He watches as one of them attacks the other two, and then realizes that it's Grant, who has already gotten inside. Grant lets Fitz in and they find the overkill device. Fitz goes to work but warns that it will take a while.
Coulson goes to the operations room and Victoria tells him that one of his team members knocked out Sitwell. He tells her that he'll do with it and demands to know why she didn't tell him the assignment was a suicide mission. Victoria explains that she didn't know if Coulson would comply if he knew, given his recent behavior. Coulson insists that Grant and Fitz had the right to make the decision for themselves, and Victoria tells him to trust the system.
As Fitz disables the overkill device, Grant tells him to leave and he'll do the rest. When Fitz refuses, Grant tells him that he couldn't make contact with the exfil team and they're on their own. Fitz figures that Grant thinks that he's a coward and insists that he's just as much a S.H.I.E.L.D. agent as Grant is. Grant figures that Fitz is still upset that he didn't have the chance to save Jemma when she was infected with the Chithauri virus, and tells his friend that Jemma knows he would have. Fitz tells Grant that Coulson asked him to take care of Grant, and that he isn't going anywhere until the mission is completed.
Skye, Jemma, and Melinda go aboard the transport and start planning their own extraction. Coulson is waiting for them in the cargo hold and tells them that he's in on the mission, book or no book.
Fitz removes the key component from the overkill device and Grant sets off the remote beacon. Victoria and her team pick up the signal and order an air strike.
At the compound, the alarms go off as a missile hits the building, and Grant realizes that the assault has begun. Fitz uses the trigger device to set off the separatists' weapons as they run in, disabling them, and Grant takes all of them out except one. The last soldier gets the drop on him and Fitz finally knocks the man out from behind. They run out only to find themselves surrounded by more separatists. However, Melinda brings the transport down low and uses the backburners to knock out the soldiers.
At The Hub, Victoria receives a report that Coulson's team is successfully extracted. When Sitwell points out that there wasn't supposed to be an extraction, Victoria says that they needed the resources elsewhere... but Coulson didn't.
As they fly back, Grant and Fitz thank Coulson for the rescue, and he assures them that they take care of their own. Jemma asks Fitz about the sandwich and he lies, saying that it was delicious. Skye congratulates Grant and admits that she was worried that she might need a new SO, and Grant tells her that he was in good hands. Meanwhile, Fitz asks Jemma if anything exciting happened to her and she admits that she shot a superior office.
Later, Coulson talks to Skye and tells her that he checked The Hub's computers and found a redacted file about her parents. The only part he could read says that the person who dropped her off at the orphanage was an unidentified S.H.I.E.L.D. agent. S.H.I.E.L.D. has no idea if it was Skye's mother or someone else. Coulson assures Skye that he's put in a request to get more information and she hugs him in thanks.
When Coulson returns to his office, he finds Melinda reading the file. He tells her that he told Skye the truth, much to her surprise, but admits that he couldn't tell her why because some secrets are meant to stay secret. Coulson asks Melinda to help him find out what really happened and she points out that it could be dangerous, but agrees to help. She then glances through the file, which contains a photo of the S.H.I.E.L.D. agent... shot to death. Meanwhile, Coulson steps away and calls The Hub for information on his recovery in Tahiti. When he gives them his security clearance, they tell him that it's not high enough for them to provide the information.