The narrator reads a long, boring story about the existence of an ancient Native American civilization which disappeared for unknown reasons.
Present Day. Edward Carnby (Christian Slater) is on board an airplane and has a nightmare, in which he remembers how he hid himself in a high-voltage box as a child, while staring at some alien-like creatures.
As an adult (explaining in a voice-over narration), Edward looks for remains of an extinct Indian tribe, the Abkani, which disappeared suddenly 10,000 years ago for reasons unexplained. He's found a trinket piece of something related to it. On his way to the museum where Aline Cedrac (Tara Reid), an assistant curator and Edward's ex-girlfriend, works and is scanning some more Abkani pieces, he is attacked by somebody with supernatural abilities named James Pinkerton (Ed Anders) who tries to steal the artifact that he has, but Edward fights him off.
At the same time, Professor Lionel Hudgens (Matthew Walker) almost doesn't make it alive from a sea voyage, where he finds the "edegus" or something like that. The ship's crew finds a coffin made of gold from the ocean floor. After they dock, the evil and greedy captain of the salvage tug locks up Hudgens and his men open the gold coffin... even though Hudgens asks them not to do so. Five minutes afterwards, they are all dead but for Hudgens, imprisoned inside a storage room on the ship. Hudgens slips away ashore after collecting another item from the empty gold coffin, which apparently contained a mysterious creature.
Upon the opening of the gold coffin, an old friend of Edward disappears into the night. Several other people across the USA and Canada walk off in a trance as if being drawn by some beacon. Edward hears a ear-splitting screech while in his apartment looking over the Abkani artifact. At the same time in an underground military facility, called Research Agency Bureau 713, the location of the opening of the gold coffin is relayed by the control room techs who report it to their bureau chief by the evidence of the electro-magnetic wave that appears on their monitors.
Edward, a paranormal investigator and former agent of Bureau 713, thinks it's related to the Abkani. The old friend was a fellow orphan, from when Hudgens convinced Sister Clara (Karin Konoval) to run some experiments on the children without anybody's consent (shown in another flashback). Edward investigates.
Edward arrives that same evening at the Natural History Museum where he is reunited with a not-so-happy Aline with the artifact and she shows him another Abkani artifact that recently arrived and she has been working on it since Professor Hudgens is away. Just then, the mysterious creature from the ship attacks them inside the museum, killing a security guard, but Edward and Aline hide in a storage closet long enough for troopers from Bureau 713 to arrive, and the creature (which is a four-legged, fast-moving beast resembling a cross between a panther and the creatures of 'Aliens') retreats into the night.
Commander Richard Burke (Stephen Dorff), the team leader of the Bureau 713 strike force, arrives where Edward tries to relay information to him that something big is going down, but Burke rebukes him, saying that since he no longer works for Bureau 713, to stay out of their investigation.
The next day, Edward tries to get information from his former co-workers at Bureau 713, one of whom is staff surgeon and pathologist Sam Fischer (Frank C. Turner), to learn more about the creature encountered as well as the history of the Abkani.
At the same time, Professor Hudges arrives back at the museum where he goes to his office where he has a captured creature (whether this is the same creature from the ship or a different one is never fully explained). Hudgens uses a syringe to draw fluid from the captive creature to study it as part of his further research to combine the DNA of man and beast.
Edward continues investigating his past by going to his former orphanage to learn more about Hudges research, and then back to his apartment where Aline is and they consumate their attraction to each other.
While the Bureau 713 soldiers are patroling the museum, they are attacked by several creatures, who are the missing people that wondered off upon the opening of the gold coffin containing the creature. During the firefight, several soldiers, and most of the human-creatures are killed. Edward arrives on the scene and talks more with Burke, who again tells him away. However, during a scuffle, Edward picks Burke's pocket containing his Bureau 713 security badge.
The next morning, Edward goes to Bureau 713 where he talks with Fischer in the morgue looking at one of the dead bodies, where Fischer shows Edward a small, cenntipede-like baby creature in the dorsal spine of his old friend Pinkeron. Fischer also discovers that Edward has one of his own in his body, but it is dead, presumably because of the contact with the electro-shock while Edward was a child. Fischer tells him that he could take the creature out, but leaving him disabled. As the monster looks dead, it's not an urgent matter. Burke and his men arrive and escort Edward out of the morgue and the building.
That evening, Professor Hudges ambushes Fischer as he arrives home to find his wife dead. Hudges inserts a baby creature into Fischer's mouth, thereby putting him under his control.
Edward discovers that the Abkani had fought those creatures which can get killed by light (that's why they always move around on dark places). They also disrupt electrical light, creating blackouts. The Abkani artifacts found all over the world actually open the gate to another dimension, where millions of those creatures are sleeping, waiting to be freed and kill humans. Hudgens is making further experiments with the creature he's captured somehow when he takes some of the creature's blood and injects it into his veins. That way, he becomes a semi-alien being and can control the monsters.
At the climax, Aline, Edward, Burke and the latter's military squad go to Edward's orphanage, where there are strong electro-magnetic disruptions. They are attacked by dozens of these reptilian-like monsters and there is a climactic and violent 20-minute fight where almost all creatures and humans kill one another. Edward, Burke and Aline reach the old surgery room underground where the baby creature was transplanted into Edward. There, Hudgens takes Edward's piece of archeological remains and opens the gate. Millions of creatures start to wake up and run down a huge cave. They go down the walls but they don't approach the gate for some reason, giving time for the three good characters to kill Hudgens, run away only to realize that they can't detonate the bomb from such a long distance. Burke comes back and blows everything up... himself along with the creatures.
Edward and Aline rise to the surface at the back of the orphanage at dawn, only to find an evacuated city without people, cars abandoned on the streets. They walk down the street, but several noises are heard. The last shot shows them in the middle of an empty road turning around suddenly, supposedly to confront one of the creatures.... regardless of it being day.
Aren't the monsters hurt by light? Because the gate hasn't been closed properly, the door has been left open for a second installment. (No, please!)