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Mike Peterson and his son Ace are looking into a shop window at toys. Behind them, a building explodes. Hiding his identity under a hoodie, Michael scales the wall, rescues someone inside, and leaps out of the fifth story window, saving the person before leaving the scene. Skye is standing nearby filming his heroics with her cell phone.
In Paris, France, Grant Ward uses his agent skills to break into an apartment to retrieve a Chitauri neuro-link but the woman living there has a couple heavies fight Grant, but he takes down both and hitches a ride on a S.H.I.E.L.D. helicopter. Maria Hill debriefs him on his mission and makes sure Grant truly understands the purpose of S.H.I.E.L.D. He questions why he was pulled out of Paris to which she says to ask Coulson. He claims that, because he is level 6 clearance, he knows Coulson had died. Coulson soon steps out and reveals that Grant is now level 7. Coulson shows Grant videos of superheroes that need to be tracked down and commissioned by the agency. Grant says he doesn't work with others: Coulson checks his file and says his combat and espionage skills are superb but he lacks people skills.
Skye follows Michael to a diner to confront him of being the "hooded hero". He claims to be a regular guy but she sees him as a hero and says he's in danger of S.H.I.E.L.D. hunting him down. She says if he reconsiders, she will be in her van around the corner.
Coulson goes to Agent May but she says she does not want to return to the field. He tells her all she has to do is drive the bus. Jemma Simmons and Leo Fitz, two inseparable physicists, upgrade the Agent ID chip in his phone for his new clearance. Agent May takes off with the agents to find Skye, broadcasting a rebellious message in her van. After taking her in to the interrogation room, she says she actually wanted to be in their headquarters. They try to get her information on the hooded hero. The two agents leave the room and return with a truth serum, but Coulson uses it on Grant, who begins blurting out the truth.
May, Simmons, and Fitz return to the scene of the earlier explosion in order to investigate. They discover a lab, now charred. Fitz releases robots to search the lab. The robot (called Bashful) finds a security camera, which Fitz will be able to use to find out what happened in the lab.
Michael asks someone on the phone what Project Centipede is, revealing the source of his power. In the factory, Michael's boss makes him angry because he won't give him his job back. He begins tearing things apart and even tosses the boss. He calls his boss the "bad guy" and equates himself to the hero.
Using Michael's ID that Skye stole earlier, they find out who he is and must find him because he appeared on the news for his actions at the factory. The agents get to work on tracking him down and find out what went on in the lab.
Michael visits the scientist he saved but she is mad that he came the hospital. It is revealed that he was a test subject for Project Centipede. She tells him that he, Mike Peterson, must disappear, just before he escapes by jumping from the hospital window.
Based on the footage from the camera, Fitz finds out more about Project Centipede. Winding the tape to the video before the blast, they discover that another Project Centipede test subject blew up the lab... with himself. They set out to save Michael before he explodes also. They either have to kill him or destroy his implant. Coulson says he cannot die for his son's sake. Fitz and Simmons develop a serum that will save Mike.
Mike, with Ace, comes to save Skye from the men in black suits. He has Skye erase all of his information but she gives S.H.I.E.L.D. a heads up where they are. Coulson and Grant show up to save him but he becomes hostile and fights some thugs but he is indestructible. Grant is even unable to take him down. He is shot and falls over the edge of a tall drop but is unscathed. Coulson confronts him, putting his hand gun on the ground. Grant is ready to shoot him with a sniper rifle. Mike begins calming down after Coulson negotiates with him, and Grant shoots Mike with the serum bullet Fitz engineered. Michael is still alive and saved from the poison of Project Centipede.
Skye tells Ace that his father will come home. She and Coulson sit in his car and he asks if she wants to join the agency. He gets an "0-8-4" alert and only gives her ten minutes to decide if she wants to join, as his car lifts off much like an airplane.