Plot

S.H.I.E.L.D. puts together a special team, led by Agent Phil Coulson, to track down a mysterious man with special abilities and the young computer hacker that's encouraging him to reveal himself to the world.

A voice over criticizes those who would hide the truth from the public and notes that the world is full of wonders.

On a city street in LA, a man and his son Ace stand outside a toy store filled with toys based on the Avengers. The man explains to his son that he hopes to find work soon after having lost his job at the factory. Just then a nearby building explodes. Leaving his son with a friend, the man rushes to see if he can help. Hearing a cry for help he rushes into the building and uses superhuman strength to pull a woman free. He then leaps out of an upper story window to the street below. Although his face is obscured by the hooded sweatshirt he wears he is recorded by several people, including a young woman.

SHIELD agent Grant Ward rides a motorcycle through Paris. He is informed that the group Rising Tide has published the location of the artifiact he seeks and that others will soon be arriving to find it. Posing as a waiter he obtains fingerprints from a drink glass used by his target. He then uses the prints to gain access to an apartment. Discovering a false room behind a fireplace he retrieves the object. However, he is discovered and attacked by two men. After defeating them in a fight he escapes by helicopter.

Ward is debriefed by SHIELD director Maria Hill. She asks him about what he sees as the group's mission. He says that they exist to protect the world from the "weirder world" for which they are not ready. When he asks why he was pulled out of Paris, Hill tells him to ask Agent Phil Coulson. Ward says that he knows Coulson was killed before the Battle of New York. He is surprised when Coulson steps from the shadows, very much alive.

Coulson explains that he was dead for eight seconds before being revived. Director Fury, seeking to unite the Avengers, took the opportunity to fake Coulson's death. He spent several months recuperating in Tahiti and is now back with a new assignment: to deal with the weird events which trheaten mankind and to ferret out Rising Tide, a group of hackers who have shown unusual talent and an interest in superhumans. Their first assignment is the "hooded hero" who rescued a woman from a burning building in LA. Coulson wants to use Rising Tide to get to the new superhero. Ward is assigned to Coulson's team, over his own objections that he is a combat operative and not suited to the job. Dr Strieten arrives and lets Hill know that Coulson's team have all been cleared for duty. But he advises Coulson that he should rest up some more. Coulson replies that he had enough rest and advises that Hill should try going to Tahiti, which he descibes as "a magical place." After Coulson leaves Streiten says "He really doesn't know does he." Hill replies that "He can never know."

In LA the man from the explosion walks down the street, reading a newspaper account of the incident which describes him as the "hooded hero." He is observed and followed by the young woman who recorded his heroics. She approaches him in a diner and introduces herself as Skye. She tells him that he should be exploiting his newfound fame and warns him to be wary of SHIELD, which will seek to contain him. She offers her own help in protecting him from the people who she says will come after him. When he goes to leave, she swipes his driver's license and sees that his name is Michael Peterson.

Agent Coulson approaches Agent Melinda May, who works in a cubicle processing paperwork. She says that she doesn't want to go out into the field again, but Coulson insists that he just wants her to "drive the bus" and provide some supervision for the younger agents.

Agent Ward boards the converted transport plane which will serve as their mobile command unit. There he meets Fitz and Simmons, the technical duo for the team. Coulson arrives in his vintage car, named Lola, which Fitz says is equipped with lots of old school SHIELD technology. Ward meets Agent May and is surprised that she is merely serving as their driver.

In her van, Skye conducts an internet broadcast on behalf of Rising Tide. She defiantly claims that they will never be found. Just then, Coulson and Ward open the door to her van and Ward pulls a bag over her head. Coulson and Ward interrogate Skye. Coulson asks her about the hooded hero and how she got onto him. Ward suggests that maybe she blew up the lab to draw him out and she replies that maybe SHIELD did. She notes that they've covered up things before and suggests that they are covering up Centipede. She then realizes that Ward and Coulson don't know what Centipede is.

Meanwhile, Mike calls the doctor who gave him his powers and tries to convince them that he should go public. But the doctor refuses. Fitz and Simmons arrive at the burned out lab with Melinda May. They deploy a series of quadrotor drones to analyze the lab and discover the remains of a security camera and a burned alien artifact.

Back at the plane, Coulson pulls Ward out of the interrogation. Coulson believes that Skye is an asset. He explains that they know nothing about her and the fact that she has been able to hide her identity from them proves that she has skills they can use. He and Ward re-enter the interrogation room where he shows Skye a new top of the line truth serum which will make it impossible for the subject to lie. He then injects Ward with the serum. To earn Skye's trust he leaves her alone with Ward to give her the opportunity to ask whatever questions she wants.

Mike returns to his old factory to try and get his job back. However, his old boss refuses. Mike gets angry and beats up his boss. On the plane, Coulson shows Skye security footage of Mike attacking his boss. Fitz and Simmons have gotten a picture from the lab's security cameras of an angry confrontation between two men. Skye offers them audio which she recorded while she was conducting surveillance on the lab.

Mike goes to the hospital to visit the woman he saved. It turns out she is the doctor who had experimented on him. She describes the people who gave her the technology as very dangerous and she's worried that he's exposed her. She also worries that Mike's mental state is deteriorating due to the treatment, just as it had with a previous subject.

Using Skye's audio, Fitz manages to reconstruct a 3d video representation of the man who caused the blast. He had an angry confrontation with one of the doctors. The SHIELD team notices a centipede like device on his arm. Simmons says that it's an alien blood filter which is delivering a serum similar to the super soldier serum which Dr Erskine worked on in the 40s. They determine that the new serum, which they dub extremis, actually caused the previous subject to explode and that Mike is in danger of doing the same. Fitz and Simmons determine that the only way to stop Mike from exploding will be to kill them. Coulson angrily tells them to work on another option.

As Skye prepares to leave her van, Mike appears and knocks out May. He has his son Ace with him and forces Skye to drive them to the train station and use her computer skills to create new identities for him and his sons. As Fitz and Simmons work frantically on a way to stop Mike, they discover that their secure channel is being hacked. Coulson recognizes it as Skye's work and that it provides them with her location. He and Ward approach Skye's van and try to talk to Mike but he knocks them down and flees with Skye and his son. As they make their way through the crowded train station, Skye provokes a fight with a group of men and they attack Mike. Coulson uses the distraction to get Ace away from the scene. Meanwhile, Mike's doctor shows up outside the station and sends an armed man disguised as a police officer into the station to kill Mike. The man shoots Mike, knocking him off a balcony. He then takes aim at Skye but is subdued by May.

Coulson confronts Mike who thinks that SHIELD will try and kill him. Coulson insists that they're only trying to help and tries to convince Mike to do the right thing. Mike wonders what ordinary people are now that "giants" walk the earth. Coulson says that he's seen giants up close and that it almost cost him everything. He reminds Mike that what makes them heroes is not the abilities they have but what they choose to do with it. Mike says that he wanted to be a hero and Coulson replies that he's counting on that. Just then, Mike is shot by Ward. Simmons rushes forward and assesses that Mike is still alive. She and Fitz had succeeded in creating a tranquilizer formula which would incapacitate Mike and stop his explosive reaction from building.

Skye and Coulson drop Ace off with a foster family. Coulson tries to convince Skye to join their SHIELD unit, saying that they will be investigating the weird things which she always wanted to discover. Ward calls them and says that they've got a report of an "0-8-4". Sky asks what an 0-8-4 is and Coulson says she's got ten minutes to decide if she really wants to know. When she notes that there's no way they can get to the airfield in ten minutes he flips a switch and Lola transforms into a flying car.