Thirteen-year-old Colin Wagner anticipates Mystery Day celebrations with his friend Danny Cooper and other classmates. Mystery Day is a worldwide holiday that marks the disappearance of superheroes and supervillains after a great battle in Pittsburgh, Pa., 10 years earlier.
As the boys discuss celebration plans at Colin's house, Danny rescues a girl from being run over by a bus. Danny saved her faster than Colin could turn his head to see the approaching bus. Danny talks to his dad about how he rescued the girl and learns that he has a superpower. His dad used to be the superhero Quantum. Danny tells Colin the full story.
Danny's dad asks whether Danny kept his powers a secret. He then announces that he wants to show Danny something, and they quietly leave without telling Danny's mother or brother. As they walk, his father notifies a helicopter team to pick them up at the Wagners' house.
Colin's superhearing has begun to function, so he hears the Coopers talking. Colin tells his dad, his mother, Caroline and the family. They immediately get in the car and drive away. A helicopter pursues them. They manage to lose their pursuers, leave their car in drive and jump out before it heads into a tunnel. At the utility passageway next to the tunnel, Colin's dad encourages Colin to push the metal door open. To Colin's surprise, he has amazing strength and is able to force open the door.
In the tunnel, Colin is able to see in the dark and leads his family to the other side. While in the tunnel, his parents explain that they were the superheroes Titan and Energy until the evil Ragnarök destroyed everyone's superabilities with a machine. Ragnarök wanted to be the only person with superhuman abilities.
Colin learns that his parents have been hiding since the great battle. His father insists that Colin keep his powers a secret from others. The helicopter pursuing them has landed on the other side of the tunnel, and the Wagners are taken into custody without a fight.
Although the reason is unclear, Danny is unconscious and buckled to a seat in the same helicopter, which is manned by guards and the man Danny has called Dad for 10 years. Caroline tells him that the imposter Quantum must be the villain formerly known as Façade.
In an abandoned mine in the western United States, Danny's real father, Joseph, lays sedated. He truly was the superhero Quantum and had prophesied that his son would lead an army in a war that would destroy the world's population. Quantum was tortured by dreams of his superhuman visions and submitted to being sedated and imprisoned. His powers were gone, but he knew that his accomplices would break him out at the right time.
Quantum, Façade and a man named Victor Cross are working together to prevent the war that Quantum envisioned. Victor oversees technicians working in a guarded underground laboratory to develop a power damper machine that will strip the world of superpowers.
The helicopter lands at a private Florida airstrip so Façade and Victor's men can transfer the Wagners and Danny to an airplane for the final leg of their journey. Caroline whispers that if anyone has a chance to escape, he should go. Warren tells the boys that if they are able to escape, they should look for Max Dalton or Solomon Cord. Max and Solomon fought with the Wagners before they lost their powers.
At the airport, Colin manages to outsmart Victor's guards, even though his powers are no longer functioning. The powers function sporadically as they are developing. Danny is separated from the Wagners and drugged to keep him cooperative.
At the underground facility, an accident with the power source for the power damper machine causes Renata Soliz, a third superhero known as Diamond, to transform from her impenetrable solid form back into to human form. She has been unconscious and trapped in her solid state since the explosion of Ragnarök's machine 10 years ago. As she furtively explores the tunnels and hallways, she discovers the power nucleus — a large silver ball housed on the cave's lowest floor — and learns about a null field protecting it.
Renata is trying to find a way around the entrance guards when she recognizes the superheroes being brought into the cave, Energy and Titan (the Wagners). Renata transforms into a solid form and hits a guard. The Wagners can't assist Renata since their own powers disappeared a decade ago, so Renata is captured and held at gunpoint. Colin's parents are placed in an unknown cell. Danny is unconscious and taken to a lab.
Colin learns he is in Jacksonville, Fla., and takes an airport shuttle to a nearby mall. He calls a runaway shelter and agrees to spend the night there. He hopes to find Solomon Cord, as instructed by his parents. At the shelter, Colin meets an 18-year-old con man and thief, Razor, and uses his superstrength to protect himself from Razor. His enhanced hearing works again, so he finds a way to get Solomon's address in Richmond, Va., when he hears the director of the shelter on the phone with her superiors. He also hears Victor's men arrive, having picked up the police dispatch. Colin cons Razor into driving him to Virginia.
Danny regains consciousness as he is placed on a lab table in the underground facility. Various capacities must be tested and measured to calibrate the power damper machine. Danny refuses to allow the testing. His father explains his prophecy to gain Danny's cooperation with the tests. Danny refuses to believe the prophecy. As his powers begin to function again, he is able to grab a medical technician's stun gun, use it on her and the guards, and escape with one of the guard's guns. Danny runs through the cave nearly at the speed of light, testing his powers in the process. He decides to go back for his friends, so he re-enters the lab where he left his father and demands to know the Wagners' location. Danny loses his temper when his father tries to convince him about the truth of the prophecy again and strikes Joseph on the head with the heel of the gun. His father dies.
Then Danny runs. Although the guards can't see Danny because he is so fast, they shoot in the direction of his sound. Danny falls against the facility's entrance door to avoid the bullets and melts through it to the outside.
In Virginia with Razor, Colin convinces Solomon of his identity by lifting an automobile engine over his head. Solomon contacts Max Dalton, and the next day Max arrives in Richmond. He and his men take Colin and Solomon to the underground hideout.
Solomon and Colin soon learn that Max is working with Victor and Façade. Solomon is taken hostage, and Colin is captured and restrained in ways that, despite his powers, prevent his escape.
Then Max handcuffs the Wagners and takes them to the examination room where Colin is held. Max admits that he used his mind-controlling powers on Quantum to gain support for his plan. While the action between Max, Solomon and the Wagners happens, Victor kills several technicians who were working on a secret project for him, and he escapes with one technician.
When Max learns of Victor's departure, he wants to proceed with their plans anyway. The medical technician gets enough data from her tests of Colin to confirm that the power damper machine is ready to go online.
Renata eludes her guard and releases Solomon. The Wagners are with Max, attempting to talk him out of his plan to strip superhumans of their powers because the machine will kill 60,000 innocents, too. Façade agrees with the Wagners at this point and is led away at gunpoint by three guards.
In the hallway, Façade and three guards run into Renata and Solomon. Solomon knocks two of the guards off their feet and separates them from their weapons. The third takes a shot at Façade. Danny has returned to the cave and deflects the bullet heading for Façade. Solomon, Renata, Façade and Danny return to support the Wagners.
Renata lifts Colin out of his restraints, but fails to prevent Max from activating the power damper. Façade can't override the activation, so all focus turns to shutting down the machine's power source, the nucleus that Renata discovered. Colin picks up Renata in her impenetrable Diamond form and uses her as a shield against the gunfire of the automatic weapons. Danny is then able to penetrate the null force field around the nucleus by traveling at a speed faster than light. He deactivates the nucleus by melting his arm into the core of the nucleus.
Danny's quick response saves lives, but he loses his arm. Colin visits him in the hospital. Max and others at the facility are arrested.