Daniel X is a highly intelligent alien with superior strength and speed. He has the ability to create and transform the atomic structure of objects, teleport himself from one place to another and travel through time. He 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, who murdered his parents when he was a toddler. Daniel's childhood friends — Dana, Emma, Willy and Joe — were killed during an alien invasion on his home planet of Alpar Nok. He is able to bring them to life from his imagination, and they help him in his quest.
Wearing a disguise, Daniel sneaks into an abandoned coal mine in West Virginia. This is where No. 2 on The List, Abbadon, is meeting with his followers. Abbadon tells them to prepare for Armageddon, saying that humans are ripe for the taking due to divisions, greed and religious differences. Soon, all humans will hail him as their new lord and master. He tells his henchmen that Daniel X is the only one who has the power to stop him, so he orders them to find Daniel.
Knowing this will be his hardest assignment yet, Daniel decides to summon his friends while at an amusement park. FBI operatives led by Agent Martin Judge surprise the group at the park.
Agent Judge is with the FBI’s Interplanetary Outlaw Unit (IOU), which functions as a liaison between the United States federal government and visitors from other planets. He worked with Daniel’s parents to eradicate alien outlaws. Agent Judge asks for Daniel’s help to eliminate Abbadon. He invites Daniel back to his ranch in Kentucky, where Daniel meets Xanthos, an alien who looks like a thoroughbred stallion.
Xanthos was the spiritual adviser to Daniel’s father. Telepathically, the alien horse communicates to Daniel that his mission to take on Abbadon will be the final battle. Daniel disagrees, saying the final battle will be with The Prayer when he takes revenge for his parents’ murders. Xanthos warns Daniel against giving in to hate and anger, but Daniel ignores his advice. Daniel also meets Melody, Agent Judge’s teenage daughter, and is immediately attracted to her.
While at the ranch, Daniel learns that Abbadon has attacked Washington, D.C. Abbadon announces on television that if people wish to survive, they must join him underground. Daniel watches as people stampede to the underground entrances of the metro system, while others take advantage of the chaos to loot and riot. Abbadon revels in the indifference humans show to each other.
Along with his friends and Agent Judge’s team from IOU, Daniel travels to the nation’s capital. Daniel and the team start fighting Abbadon’s henchmen, locust-like aliens who are destroying the city. The fight ends when Melody blasts an ultrasonic frequency that kills the henchmen. At Abbadon’s prompting, the president of the United States then appears on television, asking people to comply with Abbadon’s demands and for Daniel’s surrender.
After destroying Washington, D.C., Abbadon appears in four cities at the same time: New York, Beijing, London and Moscow. Posing as the Four Horsemen of the Apocalypse, he calls for people to serve him and live, or refuse him and die. Millions bow down and pledge their allegiance. Using a clue revealed by Xanthos, Daniel realizes the real Abbadon is in New York. After teleporting into the midst of the ruined city, Daniel sees Abbadon herding people down staircases to subterranean train tracks.
Daniel confronts Abbadon. Despite Xanthos’ warning about giving in to anger, Daniel challenges Abbadon to a fight. When the alien hits him, the impact sends him a day into the future, where he sees New York is completely destroyed. He also sees a homeless man, who says that yesterday was the end of the world. The man quotes Revelation 6:4, which tells of the rider of a red fiery horse being given the power to take peace from the Earth. Daniel travels one day back in time to the ranch to ask Xanthos for advice. Xanthos says that Abbadon came to Earth to destroy it. When Daniel asks how to destroy the alien, Xanthos says it is better to build up than tear down.
Abbadon attacks the ranch, kidnaps Melody and sets the barn on fire, killing Xanthos. Abbadon then sends an alien to negotiate with Daniel, telling him that Melody will only be released if Daniel surrenders. Against Agent Judge’s wishes, Daniel agrees.
The night before he leaves to face Abbadon, Daniel’s father, Graff, appears to train his son for the battle. The two spar viciously, and Daniel becomes increasingly angry with his dad. Graff warns his son not to give in to hate and rage, telling him that Abbadon wins by making his targets slaves to those emotions. He says throughout history, whenever humans are fueled by ignorance and hate and turn against each other, Abbadon is behind it.
Graff also says that Abbadon is the alien he was preparing to battle when No. 1 killed him. When Daniel demands to know Abbadon’s identity, his father says Abbadon is the Prince of Darkness, Satan himself. He says that Daniel must fight him, as this is the ultimate struggle between the creator and destroyer, a clash that is recorded in holy texts on every planet in the universe.
With a group of IOU agents and his friends, Daniel heads to the abandoned coal mine in West Virginia. Along the way, several die or are hurt. Daniel realizes that he and Abbadon command the same incredible powers, so Abbadon can use his imagination to destroy whatever Daniel creates. As Daniel considers his ability to make people see things that aren’t really there and believe things that aren’t really true, he wonders if the world really is destroyed in the future as he witnessed, or if Abbadon planted those images in his head.
Graff tells his son that he must find a way to destroy Abbadon. When he does, he will complete their family’s mission on Earth. Since his mission as Daniel’s father is complete, Graff says his spirit must move on. After Graff’s image fades, Daniel’s mother appears to him and then disappears as well. Daniel is heartbroken.
The group continues until they come to the gates of hell, which exude a putrid smell, noxious fumes and gaseous fire. Inside, they see trapped souls of the damned in several levels similar to the circles of hell as described by Dante in his epic poem, The Divine Comedy. Daniel notices that in every circle, consequences were paid in death for choices made in life.
Abbadon appears and sends the IOU team back to the planet’s surface. He makes Daniel’s friends vanish. Daniel tries to think of Abbadon’s weakness. He transports himself back in time, but Abbadon follows him there. Daniel then travels to Alpar Nok, where he finds Chordata, an elephant. Chordata says Abbadon is not immortal, but works for The Prayer, an evil god who has vastly extended Abbadon’s life. Chordata tells Daniel not to believe what he sees with his own eyes, because Abbadon uses fear to conjure up what looks real to people. Daniel realizes that Abbadon’s destruction will be erased if he can defeat him.
With this knowledge, Daniel travels to the future to see what it looks like. Abbadon yanks him back to hell and offers to make him one of Earth’s elite if Daniel will serve him. Daniel refuses. Abbadon then transforms Daniel and Melody into burning boulders and repeatedly throws them down a cliff. When they reach the bottom, Abbadon changes them into humans who must push another flaming boulder up the hill. Daniel remembers that Abbadon is not immortal, so with all his remaining strength, he imagines Abbadon is dead. Abbadon cannot imagine himself dead, so he doesn’t fight back until it’s too late. He bursts into flames.
Released from Abbadon’s imaginings, Daniel and Melody are transported back to Kentucky to Agent Judge’s ranch. Xanthos is there, as he never actually died. The cities of the world were not really destroyed either. After everything is settled, Daniel considers the anger he has within himself and wonders if he has the potential to become like Abbadon.