Seth Dormer, Callie Hannigan, and another student go to the S.H.I.E.L.D. Academy swimming pool to relax after a hard test in the Science & Technology Division. As they come in, they notice another student, Donnie Gill, studying on the bleachers. Callie hesitates to get in with the other two, and then yells a warning when she sees the far end of the pool freezing. Her friends swim to the side and climb out, but Seth's leg is trapped in the fast-advancing ice. Donnie grabs a pole and breaks the ice, freeing Seth just in time.
On the plane, Coulson receives photos of his corpse from Nick Fury once he tells his superior he knows what happened to him. Meanwhile, the team flies to the S&T Academy to investigate the freezing incident. Fitz-Simmons confirm that the device is based on research they did during their time there, and Grant reports that it was in the filter for some time, meaning someone planted it there intending to target the three students in question. He admits that he hasn't been to the S&T Academy because he went through operations, and Skye is eager to see it. Melinda comes in and informs them that she'll be dropping the four of them off while she and Coulson continue on another assignment. She leaves and Skye wonders how Coulson is handling the knowledge of his death. Grant figures that their superior will be okay once he comes to term with it.
At the academy, the four S.H.I.E.L.D. agents find Agent Weaver, head of the Academy, waiting for them. She gives them a list of suspects and explains that she's eliminated 90% of the students as possible suspects. Fitz-Simmons go with Weaver for a lecture they'll be giving to reassure the students. Meanwhile, Grant takes Skye to the Wall of Honor memorial where the names of all the S.H.I.E.L.D. agents who have died is inscribed. Skye wishes that she was part of S.H.I.E.L.D. instead of an outsider forcing her way onto the team, and admits that she feels like she cheated. Grant assures her that all she needs is a dedication to the greater good.
As they head south, Melinda advises Coulson to put away the photos and asks if he feels better now that Fury provided them. He doesn't and puts them away, and Melinda explains that they're flying to Mexico City. The S.H.I.E.L.D. agent who left Sky at the orphanage, Avery, had a partner who survived. The partner, Lumley, disappeared off the radar but has been recently spotted in a crowd in Mexico City. Melinda figures that Lumley will realize he was made and flee the city, so they're going to get there before he can do so.
At the Academy lecture hall, Fitz-Simmons address the students and advise them not to panic. The scientists say that while typically they like to push the envelope, they should pause and take stock of the past instead.
Grant questions Seth, who claims that he doesn't have enemies. However, he says that Donnie doesn't talk much because he's too smart for most people.
As Fitz-Simmons continue lecturing about the history of S.H.I.E.L.D., Donnie suddenly yells and ice spreads across his body. He freezes solid and Fitz-Simmons, thinking quickly, manage to break a small portion of the ice and inject Donnie with glucose to keep him alive. Skye and Grant arrive in the auditorium and find another freezing device beneath Donnie's seat. When they break it, the ice covering Donnie shatters.
Entrepreneur Ian Quinn is heading for the airport when he gets a call from his contact inside the Academy. Ian refuses to accept failure and tells his contact to have the situation in hand by the time he arrives.
Skye questions Donnie, who admits that he doesn't know anyone well enough to have any enemies. Once Donnie goes back to his room, Weaver notes that Donnie is the young agent since Fitz-Simmons attended. However, he isn't applying himself and may wash out. Once they're alone, Grant figures that the students won't say anything, guilty or innocent, because they're trained to resist interrogation. Instead he asks Fitz-Simmons to take him to the place where the students go to get away from the Academy so that he can conduct his own investigation.
Coulson and Melinda take Lola to a dress shop. The owner forges travel papers and the two agents wait for Lumley to show up.
As they leave the auditorium, Grant asks Fitz to talk to Donnie, figuring that Donnie idealizes the older scientist. Fitz agrees and Grant asks Jemma to take them to the room where the students hang out. She takes them to the boiler room and Grant is unimpressed by the description, until he discovers the students have turned it into a high-tech discotheque.
Fitz goes to see Donnie, who insists that the freezing incident was just a prank. As they talk, Fitz notices several projects that Donnie is working on and says that he's impressed. Donnie sheepishly says that they're not his ideas.
As they run surveillance, Melinda tries to make small talk and Coulson wonders why she's acting so unusually, talking and pursuing the investigation into Skye's background. She admits that she's trying to distract him and Coulson admits that he's worried that the S.H.I.E.L.D. technicians might have changed something more than just his memories. Melinda assures him that he isn't any different than before, and that she would know if he was. Coulson concedes the point and says that he's glad that they're finally rooting out all of the secrets involving him and Skye. Considering that, Melinda tells her superior that she's having sex with Grant... just as Lumley comes out and Coulson goes after him. After a moment, Melinda tries to flank the fleeing agent.
Lumley ducks into an alley and Melinda catches up to him first. They fight it out and Melinda comes out ahead, and Lumley tries to take a cyanide pill. Melinda kicks it out of his hand and Lumley knocks her down long enough to climb up a fire escape. However, Coulson flies up to him in Lola and Lumley, seeing him, realizes that they're interested in the baby Skye.
Back on the plane, Lumley explains that he and Avery were part of a team that were sent into China to rescue a previous team that was recovering an 0-8-4. The first team was dead and the leader was holding the 0-8-4 in his arms: a baby. Lumley's team got the baby out but since then, they have been killed one by one. Agent and Lumley were the last survivors and Avery stole a Level 8 clearance to put the baby into the foster system, moving her between various homes to prevent detection. Shortly after that, Avery was killed and Lumley fled rather than meet the same fate as his teammates. Lumley wonders if the baby is safe and Coulson assures him that it is, and Melinda says that they're going to take the rogue agent in. Coulson refuses, saying that they'll drop Lumley off on their way back to the Academy. As he leaves, Lumley tells them that Skye is a curse and that anyone who gets near her dies. Once he's gone, Melinda warns Coulson that they can never tell Coulson what they've discovered, for her own safety.
At the boiler room, Skye chats up a bartender and learns that Callie is hoping to get assigned to a prestige position at the Sandbox. Callie lost her chance to Donnie and she was at the pool when Seth was attacked.
Fitz looks over Donnie's plan for a super-powered battery and immediately suggests an improvement, impressing Donnie. Donnie admits that he's grateful that Fitz is there because he has someone as smart as he is to talk to. Fitz tells his new friend that he went through the same thing as Donnie when he went through the Academy, and that Donnie will eventually come out of his shell. He invites the younger student to come with him to the boiler room, but Donnie says that he has some designs to work on.
Grant talks with Callie over a game of pool and suggests that he can recruit her for Operations as part of an elite shadow unit. Callie comments that the freezing device attacks were the best thing that happened to Seth and Donnie, and Grant orders her to explain what she means. The student tells him that Seth and Donnie have both been talking about meeting Fitz for weeks, even though the attacks were recent.
In his room, Donnie takes out a larger version of the freezing device.
Jemma calls to brief Fitz on what they've learned from Callie, and Fitz realizes that Donnie tricked him into solving the problem with the battery. He goes back to Donnie's room, but Seth knocks him out and tells his friend Donnie that they need to leave now and take the device with them.
Once the plane arrives, Grant and the others find Fitz and take him aboard. Skye asks Coulson where he and Melinda went, and he says that he'll tell her later. Fitz figures that Seth is manipulating Donnie into helping him, and that someone is backing them because they couldn't afford the freezing device components on their own. Skye logs onto the computer to track the purchases.
Seth and Donnie go to the Academy parking lot and call Quinn, and admit that S.H.I.E.L.D. is onto them. Quinn tells Seth that he will have to change the deal.
Skye traces the purchases to Quinn, who they faced before in Malta, and confirms that Seth's father works as a lawyer for Quinn's company. Coulson sends Fitz-Simmons to meet with Grant and Weaver and have them expand the search of the Academy grounds, and Skye asks to talk to Coulson.
Quinn refuses to rescue Seth and Donnie unless they can prove him what their device does. Seth eagerly accepts but once Quinn hangs up, he tells his pilot to take him out of the country. Meanwhile, Donnie begins to have second thoughts about what they're doing and warns that they don't know for sure if the device is safe. Seth insists that everything will work and that proving themselves to Quinn is their only chance. Donnie gives in and activates the device, but apparently nothing happens.
Skye asks Coulson why he's avoiding her and wonders if she's done something to offend. Coulson finally admits that he's been keeping secrets from her, but has realized he can't do it to her after S.H.I.E.L.D. kept the secret of his resurrection from him. He finally tells her what Lumley told them about Skye being an 0-8-4.
When they return to the plane, Fitz-Simmons check the equipment and discover that a superstorm is forming above the Academy.
Coulson comfort a shocked Skye as she breaks into tears.
At the Academy, Grant and Weaver go outside and see a storm sweeping across the campus grounds.
At the parking garage, Seth and Donnie stare at the growing superstorm in horror and realize that their device is seeding the clouds with ice particles. Hail drops from the sky and the two students take refuge in their truck until the eye of the storm passes over them. Donnie insists that they have to shut down the device, pointing out that Quinn can't pay them if they're dead.
Fitz warns the team that they have no way to stop the superstorm. At the Academy, Grant and Weaver get everyone into the boiler room for shelter, and then Grant tries to get to the parking garage to stop the two students. He realizes that it's impossible because of the high winds and Fitz says there is only one way left to get there. He has Melinda lift off in the plane and she takes them into the eye of storm to the parking garage.
Donnie and Seth try to shut down the device, but a power surge blasts Sean back and hits Donnie in the periphery. Donnie runs to his friend just as Melinda lands the plane on the roof. The team get the two students aboard but is unable to resuscitate Seth. Crying, Donnie begs his friend not to leave him while Melinda takes the plane back out just in time.
Later, Fitz wishes Donnie luck as he escorts him to Weaver and her men. When he offers his condolences, an angry Donnie says that it doesn't matter because his only friend is dead. Meanwhile, Melinda approaches Coulson and asks if he heard what she said earlier about sleeping with Grant. He admits that he did but says that it doesn't matter as long as she doesn't let it affect the team. Melinda assures him that it won't and realizes that Coulson told Skye the truth about her origins. He thought that her story had ended, but he was impressed that Skye said that her story started there, and that S.H.I.E.L.D. has been protecting her ever since, just like a family.
Skye goes back to the Wall of Honor with Grant and looks up Avery's name.
As Donnie is taken to the Sandbox for further examination, he traces a bit of frost on the window with his bare hand.
Later, Quinn calls Seth about the superstorm, but it's Coulson who answers. Coulson warns the entrepreneur that they'll blow his plane out of the sky the next time he flies over an allied country. Unimpressed, Quinn tells Coulson that the Clairvoyant says hello.