The narrator reads a long, boring story. Years afterwards, Edward Carnby (Christian Slater) is in an airplane and has a nightmare, in which he remembers (doesn't he mention once that he hasn't got any rememberings of... (it doesn't matter anyway, as one of the technicians in the extra materials says "they looked for suspension of disbelief") how he hid himself in a high-voltage box as a child, while staring at some alien-like creatures.
As an adult, he looks for remains of an extinct Indian tribe, the Abkani, which disappeared suddenly, reasons unexplained. He's found a piece of something related to it, but on his way to the museum, where Aline Cedrac (Tara Reid), an assistant curator and Edward's ex-girlfriend, is scanning some more Abkani pieces, he is attacked by somebody with supranatural abilities (Ed Anders in the role of James Pinkerton).
At the same time, Prof Lionel Hudgens (Matthew Walker) almost doesn't make it alive from a sea voyage, where he find the "edegus" or something like that. The ship crew finds a coffin made of gold, and they open it, even though Hudgens asks them not to do so. Five minutes afterwards, they are all dead but for Hudgens, imprisoned inside a room. (How he manages not only to survive, but to trap the monster and manage a fishing ship on his own isn't explained alone. Suspension of belief again?)
An old friend of Edward disappears on the night. Edward, a paranormal investigator now, 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. Edward investigates. Research Agency Bureau 713 does so as well, especially after Edward and Aline are attacked by one of the creatures at the museum. Edward used to work for them as well, and tries to get some information from ex-coworkers, Cmdr. Richard Burke (Stephen Dorff) and surgeon Sam Fischer (Frank C. Turner). Burke tells him away, but Fischer shows a baby-creature in the dorsal spine of Pinkeron. He also discovers that Edward has one in his body, but dead, presumable because he suffered an electro-shock as a child. Fischer tells him that he could take the creature off, but leaving him disabled, but it's not an urgent matter.
The films goes on and on learning that the Abkani had fought about 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 pieces found all over the world 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 in the ship at the beginning of the film. Hudges takes the creature's blook and injects it into his veins. That way, he becomes a semi-alien being and can control the monsters.
Aline, Edward, Burke and the latter's squad go to Edward's orphanage, where there are strong electromagnetic disrupcies. There is a 20-minute fight where almost all creatures and humans kill one another. Edward, Burke and Aline reach the old surgery room underground where Edward was tranplanted the baby creature. There, Hudgens takes Edward's piece of archeological remains and opens the gate. Millions of creature start to weak 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 and to realise that they can't detonate the bomb from such a long distance. Burke comes back and blows everything up.
Edward and Aline rise to the surface at the back of the orphanage, only to find an evacuated city without people or cars on the streets. They walk down, 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 being day. Aren't the monsters hurt by light?- because the gate hasn't been closed properly, leaving a door open for a second installmente (No, please!)
