In Hong Kong, street magician Chan Ho Yin is performing on the streets. A couple of teenagers dismiss his act as cheap magic, and Chan notices a woman in a flowered dress watching him. Desperate to impress, Chan suddenly summons a ball of fire on his bare hands and sends it flying, and then lets it vanish. Everyone applauds and moves on, and the woman approaches Chan and introduces herself as Raina. She asks to see the trick again but Chan says that it's not a good idea.
Raina insists and Chan agrees to show her privately. He takes her to his cheap apartment and she notices that he has Houdini posters hanging up. When Raina comments on it, Chan says that they just did tricks. He then summons a ball of fire in his hands and explains that he first gained his superpower a few years ago. Raina tells him that he has a gift and says that he should show the world what he can really do. Chan refuses but says that what happened occurred for a reason. Raina tells him that he's been chosen and asks him to close his eyes for a moment. When he does and opens them, two men with fireproof suits have entered the room. Chan manages to cut one of them with a table knife before they drag him away.
As the team is en route to its next mission, Grant plays Battleship against Skye to evaluate her thought processes. He admits that she's doing pretty well for an ex-Rising Tide hacker, as Skye beats him. Coulson and Melinda are watching them and Coulson points out that his instincts were right about bringing Skye onto the team. Melinda notes that she heard Coulson moving around and he admits that he was feeling restless. A report comes in on Chan's abduction and Coulson summons the team together. He explains that S.H.I.E.L.D. learned about Chan's abilities years ago and assigned a local agent to him as a case worker. Chan was supposed to conceal his abilities while they added him to their Index of all known individuals with superpowers. Skye is shocked to learn that they have an index and wonders what else they've been doing to conceal the truth.
Coulson gets Chan's case agent, Agent Kwan, on video as the agent checks out Chan's home. Kwan shows them the piece of material that Chan cut off in the struggle and they realize that it's fireproof material, and that Chan's abductors knew what he could do. The S.H.I.E.L.D. agents tell them that Rising Tide hacked their systems and found out about Chan, and Skye insists that Rising Tide maintains dozens of discrete cells across the globe. Coulson isn't convinced so Skye offers to trace the hack as proof of her sincerity. Grant backs her up and Coulson reluctantly agrees.
Chan wakes up in a bedroom with Raina standing nearby. She explains that she's not with S.H.I.E.L.D. and offers to help him increase his powers. Chan isn't interested and starts to leave. Raina says that he can leave, but if he does then no one will ever remember him. If he stays then his boosted abilities will make the world take notice of him. Raina suggests that he take the codename Scorch so that everyone can recognize him. Chan hesitates and then agrees to stay.
Skye traces the Rising Tide hack to an Internet café in Austin, TX. Fitz-Simmons check the times and compare them to the café's surveillance cameras, and identify the man responsible: Miles Lydon, an infamous hacker. The plane diverts to Austin while Coulson has Kwan try to find Chan. When they arrive, Grant, Skye, and Coulson go to the café. Miles isn't inside but Grant spots him outside. The hacker runs for it and Coulson tries to intercept him. However, Miles is ready with a pre-programmed gridlock program and changes the stoplights, trapping Coulson in traffic.
Miles drives back to his apartment and finds Skye waiting for him. Relieved, he thanks her for texting him a warning. She demands to know who he leaked the files to and Miles explains that he found the information and released it, just like they have both vowed to do. Skye complains that she had to risk her cover to warn him, and Miles says that he's been missing her ever since she went undercover. He kisses her and they have sex. Afterward, Skye dresses, making sure that a memory chip hidden in her bra is secure. Miles says that he could do more to help her if she sent him more info, but Skye insists that she can't risk her cover. She's still mad at Miles since his actions endangered Chan, and repeats her orders that S.H.I.E.L.D. is off-limits as long as she's working with them. Skye insists that they're good people and prepares to leave... and finds Melinda waiting out in the hallway.
Once Skye and Miles are secured, Coulson interrogates them and demands to know what they were up to. Skye explains met when they were going through some issues, and that they looked after each other. When she texted Miles, she was still looking after him. Coulson doesn't believe her claims that Miles is harmless and asks who he is working for. Meanwhile, Fitz and Jemma work on Miles' computer and Fitz worries that Skye wasn't honest with them when he thought that they were friends. Jemma realizes that Skye is more than a friend with Miles.
Melinda takes over interrogating Miles, who insists that he doesn't know anything about Chan. After searching the apartment, Coulson tells Melinda and Grant to take the prisoners with them. A disappointed Grant escorts Skye out of the apartment.
In Hong Kong, Raina takes Chan to a lab and explains that they plan to give him a booster that will enhance his powers. Once he receives the injection, Raina invites Chan to use his powers and he generates a massive fireball. Triumphant, he insists that no one will ever hold him back.
As the team flies to Hong Kong, they toss Miles and Skye into a cell. Skye defends her teammates actions, pointing out that Chan's life is at stake. Coulson and the others listen into their conversation and Grant figures that Miles is up to something crooked, but Fitz-Simmons can't find anything in his record. Melinda visits Coulson, who admits that he went with his guts instead of his head, and figures that Skye is still holding something back. Jemma interrupts them to inform Coulson that they found something.
Once Jemma gives Grant what they found, the agent takes it into the cell and suggests that Miles tell Skye the truth. Grant then immediately tells Skye that Miles received a million dollars to hack the S.H.I.E.L.D. server and turn the information over to his employers. Furious, Skye demands answers and Miles explains that he took the money so that he could provide a decent life for himself and Skye. He says that the woman who contacted him was a rich girl wearing a flowered dress, who provided him with the S.H.I.E.L.D. computer to hack. Miles assures Skye that he checked out the woman, and figured that she was harmless because she worked for an eco-research lab that studied centipedes.
Debbie, the Centipede scientist from Los Angeles, meets with Raina at the Hong Kong lab. As they watch Chan exercise, Debbie tells Raina that the others will be pleased. She orders Raina to drain Chan and leave, and Raina releases knockout gas into the lab, rendering Chan unconscious.
Coulson figures that Centipede is planning to create super-soldier of their own and that they abducted Chan to help them. They backtrack Miles' information on Raina and confirm that she took Chan to an office building in Hong Kong. Fitz-Simmons go over the info and warn that Centipede plans to use Chan's ability to resist combustion to make a serum that prevents the Extremis serum from incinerating its users.
Raina has the technicians secure Chan and Debbie thanks him for his participation. When Chan tries to burn himself free, he only ends up burning himself. Debbie explains that Chan's blood platelets are resistant to heat, and that they took them from his body for their own purposes. The two women leave with a vial of Chan's blood.
On the plane, Coulson tells Grant that he'll guard the prisoners while he and Melinda bring Chan in. Grant says that it's his responsibility because he was Skye's SO, but Coulson says that because he accepted Skye, it's his responsibility to clean things up.
As they wait in the cell, Skye complains that Miles lied to her, but he doesn't see a problem with releasing top-secret information and making money doing it. He tells Skye that he wouldn't intentionally hurt anyone, and admits that he doesn't know who he is. However, Miles points out that at least Skye knows what to look for to find herself. Skye angrily tells him that he's not who she was looking for in her life.
Coulson and Melinda meet up with Kwan and the local S.H.I.E.L.D. team, and they track Chan's heat signature to the lab inside of the building. They break in and easily take out the guards, and free Chan. Chan glances over at the vials of the Extremis serum as he gets to his feet. Meanwhile, a guard manages to set off the security alarm, putting the lab into lockdown. As Coulson calls Fitz-Simmons for a security override, Chan injects himself with the Extremis. His powers go into overdrive and he drills a hole through Kwan's chest with his enhanced powers.
Grant gets Coulson's SOS request and releases Skye to help them.
Coulson and Melinda take cover behind some stacks, while Chan rants about how S.H.I.E.L.D. forced him to restrain his powers. Now that he's free, he promises that he'll make the world notices. Melinda calls to him in Chinese, warning him that there's no turning back if he doesn't surrender, and Chan says that he doesn't want to turn back.
Skye accesses the security systems and tells Grant that she can only access the servers from inside the building. Miles and Grant don't want to take her in, but Skye is confident that Grant can protect her.
Chan continues trying to incinerate Coulson and Melinda, who manage to flank him. Coulson uses the night-night gun, but the shells melt before they can hit Chan.
Grant fights his way past the guards, getting Skye to the building's server room.
As Debbie and Raina flee the building, Debbie calls their superiors and tells them that everything is under control. She hangs up and Raina figures that she doesn't want their bosses to know that she messed up. The temperature continues rising and Raina figures that Chan will blow up just like the other Extremis subjects.
Skye overrides the lockdown and opens the doors, and Chan slips out. Coulson calls the plane to tell Fitz-Simmons to release Miles because they need his help.
Chan finds Debbie as Raina gets into the elevator, and Raina closes the door, wishing Debbie well. Debbie pleads with Chan but he incinerates her. Coulson steps out and tells Chan that he wishes that he didn't have to hurt Chan… but he has to. While Chan is distracted, Melinda comes in behind him and injects him with a double dose of Extremis. She then joins Coulson in running off as Chan starts to overheat.
At the plane, Miles accesses the building's air-conditioning systems and reroutes all the vents to blast the fire up to the roof. Coulson and the others get out just in time as the flames burst out of the roof and across the skyline. Grant informs Coulson that Sky managed to download some information from the mainframe before they were forced to leave. Coulson looks regretfully at the wreckage and Grant reassures him that some people can't be saved. Glancing over at Skye, Coulson says that some people can if someone gets to them early enough.
Later back at the plane, Coulson tells Miles that he either has to put on a monitor bracelet or face prison time for his crimes. Miles takes the bracelet and tells him to leave. As Miles realizes that Coulson is dropping him off halfway across the globe from his home, Coulson tells him that Kwan's family appreciates the hacker's anonymous donation. The senior agent then tells Skye to go to his office as soon as she's done with Miles. Miles tells her that she's not who she used to be, and Skye tells her lover that he's not the man she thought he was. The hacker tells her that he hopes she finds what she's looking for and walks away.
Melinda and grant are drinking when Skye walks up on her way to Coulson's office. She wonders why Grant isn't there since he's her SO, and Grant tells her that he's off-duty. When she gets to Coulson's office, he says that he knows she's been lying ever since she joined the team. He tells her to explain or leave, and Skye takes out the memory chip. She gives it to Coulson and says that it's everything she knows about her parents. Coulson brings up the information and discovers that the only useful piece of information is a S.H.I.E.L.D. file that has been heavily redacted. Skye promises to keep looking no matter what, and Coulson warns her that she might not like what she finds. However, when it's clear she won't back down, Coulson offers to help. However, he gives her a monitor bracelet, the price for her having to stay. Once he leaves, Skye considers the bracelet for a moment and then puts it on.
Raina visits a man in prison, Po. She tells him that they've solved the combustion problem with Extremis but that they've run up against Coulson's team for a second time. Raina asks Po to contact The Clairvoyant and see what he has foreseen about Stage Three. Po warns her that The Clairvoyant doesn't like to be touched, and Raina says that they all have to make sacrifices for Extremis. Po compliments her on her flowered dress, saying that he likes it, and Raina says that she knows.