Ian Quinn recently spent $10 million on a purchase from a company called Cybertek. They specialize in advanced technology and research. The mystery product is being transported via train to the Italian countryside under heavy guard. Coulson believes the package is being delivered to Quinn, so the team goes undercover on the train. Ward and May play a couple, as do Skye and Fitz. Simmons gets into her role as a daughter who is angry at her absentee father. That would be Coulson.
The team's target on the train is Quinn's head of security, a man named Carlo, although they are ultimately trying to track down the Clairvoyant. Communication between the team goes down. Ward comes barreling into a deserted car to let Coulson know they've been made. The two of them jump out the back of the train. The pursuing security agents toss a grenade. It explodes into a blue mist. Moments later, the train is gone. It has vanished into thin air.
We jump back in time to see Ward fend off two Cybertek security agents. He warns Simmons to lock herself in the luggage car with Fitz and Skye while he gets Coulson. This brings us back to the present day. Coulson and Ward fear May is also no longer on the train. Their phones are dead. Armed men are on their trail. Fortunately, they find a running vehicle in the countryside. It's been hotwired. Once they get back to the bus, Coulson learns that the local law, Luca Russo, has also had his team attacked. Cybertek knew they were at the train station.
Ward is tasked with trying to analyze the grenade that was thrown at them. Too bad he and Coulson have trouble activating the holotable. Their tech troubles get put on hold during a discussion of protocol. Ward is breaking it by sleeping with May. He's warned to not let this ever put the team in danger. Moments later, Luca Russo arrives to announce that he's found the rest of the team. His declaration is cut short when a bloodied and beaten Agent May kills him from behind.
We jump back in time to see what happened as Agent May scaled the roof of the train looking for the package. She was forced to jump when armed men fired on her. She finds Coulson and Ward in a frozen state. She needs to get them somewhere safe. May hotwires a vehicle she finds in a field. It's the same one Coulson and Ward found running. May is captured and tortured by Luca Russo, who was in cahoots with Cybertek. She's able to escape and kill the escaped Luca, who was about to take down the other members of her team. Agent Melinda may was never going to let that happen.
As Coulson fixes up May's wound, he lets her know that a toxin froze them to make it seem as though no time had passed when they woke up. That's why it looked like the train had vanished. In reality, it stopped suddenly in the Italian countryside. A panicked Simmons is inside, but there's no sign of Fitz or Skye. We jump back in time to see what happened to them. They were attacked and Simmons was rendered frozen along with the bad guy. Fitz and Skye realize they must follow the package after the train stops. It leads them to a mansion where Ian Quinn has just arrived.
Skye takes out a guard with a night-night bullet while Fitz disables the cars out front. Inside the mansion, Ian Quinn is to be given the package he purchased. Skye finds something in the basement. It's a life-size container that holds a person inside. It's Mike Peterson. Skye is quickly captured by Ian Quinn, who releases Mike from his chamber so that he can be fitted with a bionic leg. That was the $10 million purchase. Mike takes orders only from the Clairvoyant, so he doesn't follow the one given to him to shoot Skye. So Ian Quinn does it himself. He leaves Skye fighting for her life alone on the basement floor.
Mike lets the Cybertek team know that they have failed. A gunfight erupts inside the mansion as Coulson, Ward and May arrive outside. They storm inside. Mike is ordered to not engage S.H.I.E.L.D. Coulson pistol-whips Ian Quinn when he realizes he's hurt Skye, who is finally found in bad shape in the basement. Simmons orders her to be put in the chamber that held Mike. This is able to stabilize Skye for now. They need to get her to a medical facility before permanent brain damage sets in. Fitz comforts Simmons while May comforts Ward. As for Coulson, he keeps vigil by Skye's side.
Mike Peterson makes his way to the outskirts of a school. His request to see his son is denied by whoever is controlling him. Mike's bionic leg has an inscription on it. There's a Cybertek logo as well as two words etched by it reading: Project Deathlok.