Pilot is the first episode of the first season of Agents of S.H.I.E.L.D.
Michael Peterson is out with his son Ace, when an explosion erupts from the top floor of a nearby building. He climbs up the outside of the building by punching holes in the brickwork and enters through a flaming window. As the crowd looks on, Peterson jumps from the top floor whilst holding a woman in his arms. Watching him is Skye, who films him on her smartphone.
Meanwhile, Agent Grant Ward is in Paris, France and pulls off a caper in which he steals fingerprints from a glass, uses them to break into a fireplace/safe and manages to fight off the hostiles that appear and quickly escape on a helicopter. Shortly after, at a secret S.H.I.E.L.D. base, Ward talks with Agent Maria Hill about the presence of beings with superpowers, including Hulk, Captain America, and Thor.
Suddenly, Agent Phil Coulson, whom Ward considered dead, enters the room and reveals that Nick Fury faked Coulson’s death in order to bring a group of superheroes now known as the Avengers together to save the planet. Coulson was sent to a grass shack in Tahiti, where he got a little time off, but he is now more than happy to be back on the job. Coulson welcomes Ward to "level 7", explaining that the Avengers only have level 6 clearanceand that the team's mission is to investigate a hacker group called the Rising Tide.
Coulson visits Melinda May, who had retired from field duty, and convinces her to join the team.
Skye meets with Peterson at a local diner and warns him about S.H.I.E.L.D., saying that they cover up superhero based events. Later as she broadcasts alone from her van as Rising Tide, Coulson opens the door and arrests her. He takes her back to a mobile S.H.I.E.L.D. base on board a plane called the Bus.
Coulson and Ward question Skye, but she is uncooperative and mentions something called "Centipede" which neither of the agents had heard of.
In order to gain her trust, Coulson injects Ward with the QNB-T16 Truth Serum and allows Skye to question him. With her trust gained, she reveals where she filmed Peterson and Coulson sends Agents Leo Fitz and Jemma Simmons to investigate the scene of the explosion. Utilizing specialized equipment, they discover an artifact in the debris and take it back to the base to investigate. Peterson returns to the factory where he used to work and angrily injures his former boss Gary, saying that he was the "bad guy" and Peterson was the "hero".
Peterson visits the woman he saved in the hospital, and it is revealed that she was the doctor who implanted the same artifact into his left forearm. He wants to go public, but she says that her backers would not like that. He claims this is all his origin story and jumps from the hospital window.
Fitz and Simmons investigate the Centipede Device and find that it is a combination of all known causes of super powers including: alientechnology, Gamma Radiation, the Super Soldier Serum, and Extremis. Meanwhile they reproduce footage from the crime scene using the flash memory of a video camera and the audio recorded by Skye who had bugged the lab. They view the events using the Echo Chamber to discover that the explosion was caused by an angry manexploding due to Extremis. The man had the device implanted in his forearm, which they recognize on Peterson due to video footage of his attack at the factory.
Skye returns to her van with Agent May to send the audio as the encryption was tied to the geolocation. Peterson abducts her and makes her delete his information from the government's systems. At the same time she hacks into S.H.I.E.L.D. systems to inform them.
Peterson and Skye are tracked down to Union Station by Coulson's team and a gunman sent by Peterson's doctor. May takes out the gunman and Coulson talks Peterson down long enough for Ward to shoot him with the Night-Night Gun developed by Fitz and Simmons.
Later, Skye and Coulson are driving Lola, Coulson's hovercraft vintage red car toward what Agent Ward called a “0-8-4,” after Coulson requests that Skye seriously consider joining the team long-term and helping them further their cause.