Daniel X is not an ordinary human teenager. He is a highly intelligent alien with superior strength and speed. He has the ability to create and transform objects, teleport himself from one place to another and travel through time.
Daniel is also an alien hunter, following in his parents' footsteps. He goes after alien criminals on Earth found on The List of Alien Outlaws on Terra Firma. He ultimately wants to kill No. 1, also called The Prayer. The Prayer is the alien who murdered his parents and burned their house to the ground when Daniel was a toddler. Dana, Emma, Willy and Joe are Daniel's childhood friends, who were all killed during an alien invasion on his home planet of Alpar Nok. He is able to bring them and others to life from his imagination, and they help him in his quest. Daniel also has the ability to create and manipulate the atomic structure of things around him.
After intercepting a message between No. 7 and No. 8 on The List, Daniel heads to Tokyo to find both. This alien couple, disguised as humans Colin and Ellie Gygax, are founders and owners of the Game Consortium (GC), the largest video-game corporation in the world. In the message, No. 7 and No. 8 discuss hunting and killing the last members of two alien species, killing Daniel and then eradicating the human species.
At the GC, Daniel sees hundreds of teens mindlessly playing violent video games. He sneaks into the back of the store, where he finds a theater filled with more brainwashed teens beta testing a new level of a popular video game. On the theater's stage are mannequins dressed like police officers and others dressed like thugs and monsters. On command, the teens grab weapons, charge the stage and destroy only the police officer mannequins. After the assault, the brainwashed players collapse on the floor. With millions of GC games and consoles in the world, Daniel realizes that the company can flick a switch and turn any player into an armed killer.
To learn more about the aliens' plans, Daniel masquerades as a window washer for a building across from the GC tower and spies on the penthouse where No. 7 and No. 8 live. To Daniel's surprise, The Prayer arrives at the penthouse and chastises the couple for hunting other alien species when the alien he really wants killed is Daniel. After ordering them to have Daniel killed within two days, The Prayer says he has put a dampening field over the planet to prevent time travel. This will keep Daniel from using his time-travel powers to escape. The Prayer also tells them that a Pleionid, the only one left of a genius, telepathic species, has landed on Earth and must be killed before it contacts Daniel. On a computer in the penthouse, Daniel notices schematics of antennas located at the Tokyo Tower.
After The Prayer leaves, Daniel is surprised to see a teenage boy, Kildare Gygax, enter the penthouse. He is No. 7 and No. 8's son, but they are not happy with Kildare's unwillingness to hunt creatures to extinction. They tell Kildare that he will lead the hunt for the Pleionid, not knowing that he has been sheltering and feeding the alien since it came to Earth.
The next day, Daniel visits Kildare's school and befriends him. Daniel is surprised that Kildare does not fight back against kids who are bullying him. Daniel realizes that Kildare refuses to use his alien abilities on humans.
When Daniel returns to his hotel that evening, his father ambushes him to demonstrate how Daniel is unprepared for this mission. Because the exhausted Daniel fails his fathers' training tests, his father asks him leave Japan. Daniel refuses to quit, but he knows he needs to be better prepared.
Daniel returns to the GC Tower, turns himself into a fly and sneaks into a meeting with No. 7, No. 8 and their alien henchmen. After following one of the hunters from the GC Tower, and then not as a fly, stealing his tracking device, Daniel summons his friends, and they access information from the tracker about the Pleionid and the hunt.
Daniel's friends beg him to call off the mission, but he waves them out of existence and heads to the school to find Kildare. Kildare is in the science lab, studying ants in a glass terrarium. He explains that ants use pheromones to lay down scents and other chemical markers that affect each other's behavior.
When Kildare leaves school, Daniel follows him onto a train and sees Kildare teleport himself off when they pass some fields. Daniel also teleports himself off the train and finds Kildare talking to the Pleionid, who is disguised as moss. Daniel turns himself into a butterfly to eavesdrop on their conversation and hears Kildare beg the Pleionid to leave the planet before the hunt starts, but the Pleionid says he must speak with Daniel. Daniel turns back into himself, but the Pleionid challenges Daniel to catch him to prove that he really is the alien hunter.
Daniel runs after the Pleionid, but he is not alone since the hunt has already begun. He follows the Pleionid to a 400-foot statue of Buddha in the Japanese town of Ushiku. At the top of the statue, the alien takes Daniel's hand and telepathically shows him how his species changes shape, makes themselves invisible and shares thoughts by touch. It also gives Daniel its abilities right before a hunter appears and tries to eat the Pleionid.
Daniel tries to save the Pleionid, but the alien tells Daniel that the world needs him so Daniel can't sacrifice himself. The creature does not put up a fight as it is eaten whole by one of the hunters. Daniel is upset, but he uses his newfound Pleionid knowledge to change himself into a pool of invisible flesh and escape the hunters.
The next day, Daniel heads to school to find Kildare, but runs into him on the street instead. Kildare tells Daniel that his father has forbidden him to attend school. As the teens eat pizza and walk around the park, Kildare and Daniel agree to start being honest with each other. Daniel tells Kildare that the hunters killed the Pleionid. Kildare tells Daniel that he knows his parents must be stopped, and he asks for a day to figure how to do it — he hopes to stop them without resorting to killing them. Kildare begins to tell Daniel that the ocean may help stop his parents, but before the teens can come up with a plan, No. 7 and No. 8 approach them in the park.
The couple reveals to Daniel that they knew he was spying on them. They are not simply individual aliens but colonial beings composed of billions of intelligent particles that can combine and take any shape they wish. To demonstrate, No. 7 and No. 8 hold hands and change their form into a massive cloudlike creature, which descends on a nearby palm tree and consumes it completely.
Daniel is shocked at the implications. This means No. 7 and No. 8 are shape shifters who are immune to projectiles. They can disperse and reassemble themselves at any time. The couple leaves, but they send their henchmen to bring the boys back to the GC Tower.
Inside the GC Tower, the henchmen start shooting at Daniel. Kildare begs his parents not to kill Daniel, telling them that Daniel had agreed to not hurt them. No. 7 and No. 8 disregard their son and shoot at Daniel with concentrated acid. Daniel barely escapes the burning liquid. In an attempt to help Daniel escape, Kildare produces a panic pheromone that causes his parents to disperse into gray clouds.
As the boys try to flee the building, No. 7 and No. 8 join together to form one giant cloud that swallows Kildare. Daniel is angry and demands that Kildare be released, but the cloud begins to envelop him. Daniel feels an overwhelming amount of pain, frustration and helplessness because he has no idea how to stop No. 7 and No. 8. When the cloud burns him badly on the leg, he passes out.
Daniel wakes up inside the head of the giant statue of Buddha. He had teleported himself out of the GC Tower right before he would have been killed. The hunters have caught up with him, so he teleports back to Tokyo. Daniel realizes that the Pleionid has given his body the ability to heal, and with renewed strength, he figures out a way to elude the hunters.
Realizing that No. 7 and No. 8 are using a relay transmitter on top of the Tokyo Tower to direct the hunters to find him, Daniel enters new coordinates to throw them off.
After he heads back to Kildare's school and feeds the teen's ant colony, Daniel notices a piece of paper buried in the sand. The paper is filled with organic chemistry formulas Kildare had been working on. Daniel is confused by most of them, but he notices that salt and water are integral to the formulas.
Daniel takes textbooks to the beach and starts studying chemistry. Before long, No. 7 and No. 8 (in the form of an enormous Godzilla-like reptile) emerges from the ocean. Daniel materializes the principal reactors from Kildare's formula and throws them in the waves. When mixed with salt water, Kildare's formula produces a gas, which interrupts the communication between all the intelligent cells in the bodies of No. 7 and No. 8. The aliens fall apart in front of Daniel, but he feels no joy in the victory, as Kildare is nowhere to be found.
Daniel had hoped that since Kildare created the formula, he would have fortified himself so he was immune to it. As Daniel sits on the beach mourning the loss of his only nonimaginary friend, Kildare appears. Yet Daniel's joy is short lived, since Kildare is dying. The young of his species can't survive on their own before they reach maturity; he needed his parents to live. Kildare collapses into black goo at Daniel's feet, just as his parents did earlier.
Daniel cries on the beach, not only over the loss of his friend, but for the loss of all the people he has cared about. After a while, he pulls himself together, grabs a handful of blackened sand and leaves the beach.