Plymouth, Massachusetts we meet Ward fifteen years earlier in juvenile detention. Ward is taken to the visitor’s room where he meets Garrett for the first time. Garrett asks if Ward knew that his older brother was in the house when he set fire to it. Garrett goes on and offers to take Ward with him, stating it will be the hardest thing he’s done, but fun. Garrett states he works for an organization that looks for young people like him. He tells Ward that he has ten seconds to decide. After some provoking, Ward says yes, and agents burst in leading their way to escape.
Fitz-Simmons and Skye watch TV in the motel and a story on Deathlok killing a drug lord comes on. They try to figure out why he would go after someone with Hydra ties, and Coulson tells them to go in the other room. Coulson goes over a diagram he has made linking Cybertek, who created Deathlok, to Cybertek selling supplies to Quinn, who worked for the Clairvoyant, who turned out to be Garrett, who planted Ward on The Bus, all to find out about GH-325. Skye implanted a Trojan Horse on the hard drive Garrett now has, linking the location of where they store the files. In order for it to work, they have to plug in a USB drive to the mainframe of Cybertek. Coulson states S.H.I.E.L.D. is no more, and their mission is unofficial. Fitz states they’re vigilantes.
On the bus, Garrett and Ward talk about the death of the drug lord in Bogota, how Ward could have just killed him with one shot. Garrett wanted it to be a spectacle, which is why he had Deathlok do it. Deathlok walks in and Garrett calls Zeller to stream video of Mike’s son to him, for doing such a good job. Ward expresses he is upset about his order for Deathlok to kill him. Garrett states he finally is getting what he wants after 25 years, and asks him to just be happy for him.
They head down to the lab and talk with Raina. She states she’s close to replicating GH-325, stating she’s uploading the data from the hard drive to Cuba, where they are headed.
At the motel, Coulson talks to Skye and Fitz at the pool and states they are going undercover to Cybertek’s office in Palo Alto. Fitz show hesitation of the plan, and Coulson states he doesn’t have to go. Fitz then starts to talk about Ward, and that maybe his being controlled like Deathlok. Skye says he’s just evil, but Fitz can’t believe that, saying something happened to make him do this. Triplett comes up with a suitcase, filled with spy gear from his grandfather, who was part of the Howling Commandos.
They open up the briefcase and Coulson quickly starts to check out all the gear, excitedly. Fitz states a lot of the gear was made to look innocent, as Skye pushes on what looks like a joy buzzer but is actually an EMP, knocking out power in a 10 foot radius. Fitz takes out a pack of cigarettes, takes one out, and it is actually a laser. He unknowingly starts to burn the curtains.
Garrett and Ward, fifteen years earlier, walk in the woods by a river as Garrett holds two dead ducks in his hand, and rifle over his shoulder. Ward expresses concern about people looking for them, but Garrett explains no one is looking for them, and the cops stay out of S.H.I.E.L.D.’s way. Garrett informs Ward he will be staying out in the woods, and will have to learn to survive. Ward complains about not having anything, and Garrett bullies him, and tells him he has to work and earn food and shelter. As Garrett pulls away in a truck, he tells Ward he’ll be back in a couple months. Garrett leaves the dog, Buddy, with him.
Coulson and May are in the Cybertek office posing as ex-S.H.I.E.L.D. scientists looking for a job. The interviewing scientists state they are underwhelmed with them, and Hydra people are usually younger, and have an open mind. In a truck outside Fitz-Simmons are in a truck, feeding Coulson and May dialogue to say.
In the front of the truck, Skye tries to locate a mainframe inside the building, but is not coming up with any location inside the building. Skye tells the team they have to stall so she can try to find it.
Fitz-Simmons feed dialogue for Coulson and May, and for them to show the scientists and Icer. The scientists are unimpressed and ask if they have anything else.
Skye gets the specs on the building and realize there is only one way in or out of the 4th floor, with reinforced doors. Skye radios to Coulson saying he and May need to get to that floor.
Coulson and May leave the interview, and are escorted into an elevator. They quickly take out the security person and get to the 4th floor. As they head down a hallway, they see another security guard. In the middle of the hallway is a red phone, and both the guard and May rush to get to it first. The guard gets to the phone first, but May quickly disposes of him before he can call. Coulson states how good it is that she’s back.
Without a key, Coulson uses one of the laser cigarettes to open the door. When they walk in, Coulson radios to Skye telling her there is no mainframe, telling her everything is hard copy, as he looks at a sea of filing cabinets. They start to look around.
On the bus, Raina talks with Deathlok, and he asks what she is doing there. She states she is wanting to know what is inside people like him, people with special powers. Looking at a blood sample on the screen, she asks him what he knows about Skye. He asks why, and she states that she thinks she and Skye are a lot alike on the inside.
May finds a drawer about Deathlok. Coulson realizes there is another drawer, and the project goes back to 1990. He pulls out the first file, and they realize Garrett was the first “reconstruction subject” and is the original Deathlok. They hear people coming and quickly put back the files.
Coulson radios to Skye, telling her to get ready for a large file transfer. When she asks how large, a window breaks from the 4th floor of the building and a filing cabinet falls to the ground. Quickly the team get the cabinet in the truck, and creating a zip line, get Coulson and May to safety.
Flashing back, we see a young Ward stranded with nothing in the rain. Flashing forward, Ward yells at Garrett that he would have let Deathlok kill him. Garrett states he knew Skye was soft and would never let that happen. He then tells Garrett he is soft too. Garrett stands up and says he doesn’t know why he ever took Ward in. Garrett coughs, and bends forward in pain. He begins to fall and Ward quickly carries him down to the lab. Ward tells everyone to get out. Ward opens a small box, and hooks Garrett up to him, telling him he will get him stabilized.
At the motel, looking at the files, the team realize Garrett is trying to get GH-325 for himself. If he can get it, and create soldiers, then so much the better. Fitz won’t let go of the idea that Ward is being controlled. Skye regrets not letting Deathlok finish Ward off, stating she was week. Coulson quickly says she has compassion, saying that is harder. As a pizza delivery person comes up, Skye walks back into the room.
The machine Garrett is hooked up to “reboots” him. Ward states that hasn’t happened that badly in a while. Garrett states it has actually been happening more and more, that his organs are failing, and that he is dying. He states the Cybertek team gives him two months at most to live.
May goes into the room to talk with Skye. Skye wishes she could not feel pain like May. May states she feels it, but hides it, and saves it. She says if she gets in front of Ward, she will unleash all of her pain on him. Coulson comes in and states tracking of the bus has ping-ponged all over the world but has landed in Havana. May says there is an old S.H.I.E.L.D. base there. Coulson states they are going to Cuba.
In the barber shop in Cuba, Garrett and Ward meet Quinn there. Garrett states Quinn is the new face of their new empire. Ward is quick to state he is a fugitive with a list of crimes. Quinn retorts that S.H.I.E.L.D. is gone, giving him a clean slate. Garrett asks if everything is going to plan, and Quinn says yes, and will be going to Washington D.C.
After receiving a call from Raina, Ward heads to the basement to talk with her. She tells Ward she thought Garrett was more about saving the “special” people than just himself with GH-325, so didn’t want to go to him about information she found out about Skye. She has second thoughts about even telling Ward and starts to walk away, baiting him. He falls for it, and asks what about her. She reveals she’s been looking at data from the hard drive about Skye’s search for her parents, and says she heard a story about a baby girl in China, and it might be Skye. She states the story is about how two monsters ripped apart a town, and people, looking for that baby. Ward asks if the monsters killed the baby’s parents, and Raina states that’s the interesting part…the monsters were the baby’s parents.
The younger Garrett finds the young Ward has survived out in the woods. Ward pulls a rifle on Garrett, and states it has been six months. Garrett states he’s been out of the country on assignment. Ward lowers the rifle and says he started to raid cabins for food, tools and a tent. He states he was going to build a cabin, and Garrett smiles telling him he knew he could do it. Garrett pulls out a gun on Ward. Garrett states it’s for his next lesson, and begins to shoot things around camp. The he hands the gun to Ward, saying it is his turn now.
In the present, Garrett asks Ward why Raina wanted to talk to him. Ward lies and tells him she questioned moving the operation to the states. Garrett says the fact that the Deathlok files were stolen fueled his decision. Raina comes over and hands Garrett a small vile, stating it is as close to GH-325 as they have, and that it should regenerate and heal cells like Coulson and Skye.
The team arrive in Cuba. Fitz-Simmons go to find the bus, and the rest go to the S.H.I.E.L.D. base. Thinking the base is empty, Skye states something in there is generating a lot of volts. Simmons calls Coulson and states they found the bus, being loaded up, and is about three hours away from their location. Coulson advises Fitz-Simmons to get out of there, and to not engage. Skye states there may be a computer inside the base still, so they can plug in the USB drive, and track where they go. They head inside.
At the airstrip, Fitz-Simmons look on as the bus is being loaded. Simmons suggests sending one of the dwarf scanners onboard so they can track them. As Fitz is headed to the car to get one, Ward steps in and blocks his way.
Flashing back ten years earlier, we see Ward and Garrett in the woods outside a cabin. Garrett explains the metal plate, saying he got injured in Sarajevo, radioed S.H.I.E.L.D. for help but no one came. He then said to himself if he made it, he would treat S.H.I.E.L.D. the same way. He goes on to reveal he works for Hydra, a secret organization, within a secret organization.
Ward brings Fitz-Simmons to Garrett on the bus. Fitz puts his hand in his pocket, and Ward is quick to stop him from pulling is hand out. Fitz reveals the “joy buzzer” and presses it, knocking out the light behind them, and taking short fusing Garrett’s side plate too.
As the bus takes off, Ward rushes to get the reboot device, telling Raina Garrett is dying, and to call Cybertek to see what can be done.
Ward makes it back up to where Garrett is. Fitz looks at Garrett and tells him he’s glad he may have killed him. He pleads to Ward to let him die. Ward tells the guards to take Fitz-Simmons and get out.
Ward shoots a deer in a flashback. Garrett tells him he’s been accepted to become an agent, but since he’s part of Hydra, he can’t ever get emotionally attached to anyone or anything, and to fight that weakness. Garrett then tells him they have to pack up…and to take care of Buddy. “That’s not a weakness, is it?” Garrett asks.
Current day, Ward has Garrett hooked up the machine. Raina comes in and states Cybertek has people waiting to help in Miami. Garrett orders Ward to take out Fitz-Simmons, for him. Again he asks Ward, “That’s not a weakness, is it?” Ward reluctantly goes, and Raina stays with Garrett. Garrett shows Raina the inside of his plate, and Raina realizes it’s her Centipede device. He says he’s too far gone, and asks Raina to give him the manufactured GH-325.
In Cuba, they look for a computer or mainframe to plug the USB drive into.
Fitz-Simmons escape from the guards, but suddenly run into Ward. They lock themselves in a cargo pod, and Fitz tries to reason with Ward, saying they are friends.
A flashback shows Ward pointing the gun at Buddy, and fires a shot in the air, scaring Buddy away.
Back on the bus, Ward realizes Fitz-Simmons aren’t coming out and starts to release the cargo pod from the plane. Fitz-Simmons desperately try to tell him to stop, with Fitz saying he knows he cares about them.
Another flashback shows Buddy running, and Garrett ends up using the rifle to kill him.
Ward states he does care, but that it’s a weakness. He releases the pod out of the plane, and it falls into the water.
Raina injects the manufactured GH-325 into Garrett’s Centipede device. Ward comes in and Garrett asks if it’s done. Garrett then convulses, then looks like he is going to explode, then starts breathing normally again.
In Cuba, Triplett uses one of his grandfather’s devices and says there’s something behind a wall. As they find a switch to open it, it is a mainframe, but the lights quickly go out. They turn around and see a Centipede soldier with the Beserkker staff.
Quinn is sitting down in Washington D.C. with an Army General and Navy Admiral, talking about super soldiers, and how little money one would cost, as opposed to the money spent on getting Bin Laden. The Army General asks if he is trying to sell them their super soldier. Quinn says no, not one, but a thousand of them. Quinn goes on to talk about the threat of S.H.I.E.L.D. and Hydra, and that they need a higher form of protection. Quinn states they have moved their operation to a new, hi-tech facility, and asks if they would like a tour.