SPOILER WARNING: This page gives away the entire plot of the show.
Scott Bakula plays Nolan Wood, a former airplane pilot who lost his license and his business after he started hearing things in his head. Programmed by The Invaders, he killed a professor connected with the ecology movement several years before, and was sent to prison. After he went to jail, his wife Amanda divorced him and married Jerry Thayer (Richard Thomas), who is an alien big shot. Amanda's and Nolan's young son Kyle (Mario Yedidia) lives with her in Barstow, CA where she and Jerry run a diner and Jerry has a tow truck business. She is pregnant with Jerry's child.
The show features the rantings of right-wing radio crackpot Randy Stein (Richard Belzer) numerous times. He complains about immigrants, pollution, laxity in the justice system, and so forth.
As the show begins, a bunch of Mexicans are seen being smuggled over the border and they witness the night sky being filled with light and other unusual activity. David Vincent, the lead character from the original Invaders TV show (Roy Thinnes), is also watching this.
At the Barstow diner, Kyle passes his time shooting flies which are thick all over a tour bus from Vegas Gold Tours that has stopped to let its passengers have a meal. All of them are eating bacon and eggs and smoking something fierce. One of the smuggled Mexicans, Carlos (Raoul Trujillo) applies for a job as a cook/dishwasher at the diner, and Jerry hires him for $100 a week plus room and board.
An "average Joe" named Marty (Dean Hill) is shown in his house listening to Randy Stein's rants. Behind Marty outside is a sinister-looking character in an orange jump suit (an alien) who is using a leaf blower.
At the local hospital, Dr. Josh Webber (Erik King) is studying cells, uttering words like "gene splice" and "DNA." Working with him in the same lab is Grace (Shannon Kenny), a blonde who has an Australian accent. Webber is black.
The next scene introduces Dr. Ellen Garza (Elizabeth Peña) who talks to some hospital employee who is reading a tabloid newspaper with an alien-related headline on the cover. Garza rushes to a storage room, where she "does it" with Webber, who is her lover.
When it is dark, Marty goes to his company in his truck to pick up some stuff in his locker room. Down at the end of a long driveway is the alien leaf blower who is (a) smoking and (b) acting all twitchy, which indicates he is "controlling" Marty. Marty drives his truck down this driveway at high speed and eventually runs into a beam which causes a huge explosion that blows him up and also blows up (though not fatally) the leaf blower.
The leaf blower is brought to Garza's hospital and is treated by Webber. When the leaf blower dies, he "disappears" with a glowing light, after which flies are found on the hospital bed. Two cops, Lieutenant “Mac” Coyle (Terence Knox) and Detective Rudnik (Channon Roe) interview Webber, who cannot explain what happened.
Nolan Wood is seen in prison on the day he is being released on parole. He is having visions, not only of his former wife and son, but also of what looks like travelling down a subway tunnel. Once freed, he hitches a ride to Barstow in a commercial truck. Prior to getting in the truck's cab, he looks stunned, as if he cannot adjust to being out of jail.
Dr. Webber analyzes a sample of blood he took from the leaf blower before the alien vanished, and notes that its properties suggest the alien was "immune to everything." Because he doesn't trust what will happen to the sample, Webber later takes it home and puts it in his refrgerator, saying it "doesn't conform to any blood type I know of."
Coyle and Rudnik interview Marty's wife. She tells the cops that Marty had "changed," and was "seeing things in his head." The cops suggest that Marty had explosives in his truck, but the wife insists that Marty was "just a normal guy." The wife is smoking, which suggests she may be an alien.
Nolan makes it to Barstow, where he visits his wife, who is not happy, because she has a restraining order against him. Jerry gives Nolan some money to get rid of him. Amanda tells Nolan that she doesn't think Kyle recognized his father.
David Vincent is seen in the diner as Nolan leaves to be driven to Los Angeles by Monck Patterson (Jack Kehler), who is an alien. Patterson drives Nolan to a bar where Webber and Garza are hanging out, and tries to make Nolan shoot Webber. Nolan won't do this, so Patterson takes the gun and shoots Webber in the head himself, then shoots Nolan. Nolan grabs the gun and shoots Patterson, who dies nearby on the sidewalk and disappears (though this is not actually seen).
When the cops grab Nolan, the evidence makes it pretty clear what happened, especially since Nolan's prints were all over the gun, though Nolan protests that the aliens “make me do things." During the subsequent investigation, Amanda says that Nolan was "mentally ill" and "unbalanced." In a flashback, Nolan is seen in prison, being probed by aliens while sitting in a dentist-like chair.
Nolan is locked up in an isolation ward in the hospital where he is taken to attend to his gunshot wound. David Vincent is seen looking in the window of Nolan's room (there is no explanation as to how Vincent can pass security to do this). Garza comes to treat Nolan (she later tells the cops she wanted to kill him). Nolan tells her he doesn't want to dream and mentions flies which were everywhere in the truck as he was being driven to Los Angeles. This makes Garza suspicious, since Webber earlier mentioned the flies on the bed after the alien vanished.
Garza goes to the scene where Webber was murdered, and sees flies all over the sidewalk where Patterson disappeared. She scrapes a sample of the blood and brings it back to the lab and asks Grace to test it. Grace looks at the sample under the microscope and acts as if there is something unusual about it.
Back in Barstow, Kyle follows Jerry, who goes into the garage connected with his towing business near the diner. Through a window, Kyle sees Jerry inhaling carbon monoxide fumes from the exhaust of a tow truck.
At the hospital, Nolan manages to overpower his police guard, and escapes wearing the guard's uniform. Once in the parking lot, he hides under a large truck that is leaving and evades the police who are searching for him.
After getting some clothes and cleaning up, Nolan makes his way to the office of Vegas Gold Tours (a peculiar building shaped like a ship) and buys a ticket. to Las Vegas.
Meanwhile, Garza discovers that the blood sample which King left in the fridge has disappeared. When she asks Grace if she knows anything about this, Grace says she knows nothing (Grace actually took it after Webber was shot and she was consoling Garza). Grace also says that she tested the blood from the sidewalk again and it was normal.
Nolan boards the bus to Las Vegas. All the other people (passengers and drivers) are smoking. Before they get to Barstow, an alien comes on board and sprays all the passengers with gas.
At the diner, Kyle overhears Jerry on the phone. Jerry is swatting flies which are landing near him as he is talking. When Garza goes home, she finds her phone covered with flies as well. The gas is leaking from her stove, and when she leaves the apartment, it is destroyed by a violent explosion.
After he is gassed, Nolan is taken off the bus and tortured more by the aliens, including an octopus-like creature which attaches to his face and a glowing probe.
Tipped off by the fact that Nolan used a stolen credit card to pay for his ticket, the cops meet the bus which shows up at the Barstow diner, but Nolan is not on it.
Jerry leaves the diner in a tow truck, and Kyle hides on the back of the truck.
Garza shows up at the diner, and talks to Carlos in Spanish. Carlos says that things happening there recently are "strange." Amanda is concerned about the fact that Kyle has disappeared.
In the middle of nowhere, Jerry meets the tour bus and he and all the bus passengers witness a spectacular light show in the sky as the aliens come to earth. The aliens and passengers are taken to what looks like an abandoned airplane hanger, where the humans are placed in booths in front of aliens who are lying on tables. The humans get all twitchy as their bodies are swapped with the aliens in front of them.
As Nolan waits on the bus with other passengers, including the alien whose body is to be interchanged with his, Kyle sneaks on to the bus and sings a song that he used to sing when he was a little boy. This snaps Nolan out of his alien-induced trance, and the two of them escape into Jerry's tow truck which is parked near by. Kyle yells at his father to kill the aliens, but whenever Nolan approaches the jury-like box where Jerry and other alien spectators are sitting watching the transformations, the aliens get twitchy to stop Nolan from completing his task.
Finally discouraged from killing the aliens, Nolan and Kyle escape from the building by driving through a wall. On the road leading away from the hangar, they run into David Vincent, who joins them and tells them of his quest to alert the world to The Invaders. Vincent says the aliens "want us to ruin the earth for them," and say that Nolan is an "implant." Vincent suggests that because Nolan was autistic as an infant, the aliens' programming is not working as it should. Vincent leaves the truck, but not before giving Nolan his journal.
Nolan returns to the diner, and tells his ex-wife that "Jerry isn't who you think he is." The police show up almost immediately, and Nolan escapes out the back door. Minutes later, he is captured by the cops. As Nolan is taken away, Kyle tries to tell Coyle that Jerry is an alien, but Coyle doesn't believe him.
Garza, who now lives in a flophouse hotel, reads Vincent's journal which she retrieved from the tow truck. She calls Coyle, who tries to trace her call, but is unsuccessful. Garza goes to Vincent's house, which is a dump in San Pedro with newspaper and magazine clippings about aliens and invaders all over the walls, including a clipping about the murder of the professor that Nolan committed years before. Garza has to get rid of her car, so she buys a used Pacer.
Nolan is taken to the hospital when his court-appointed lawyer wants him to have an MRI to determine if there are any legal grounds for a defense of diminished capacity, considering Nolan's past history of autism, visions and chronic dizzy spells. The tests are administered, but two experts say there is nothing wrong with Nolan. Garza manages to observe the tests and later, with the help of her friend Ellen, smuggles Nolan out of the hospital on the pretext of giving him X-rays.
Coyle talks to Grace, trying to find out where Garza has gone. Grace suggests Mexico, but Coyle says this is unlikely, because Nolan wants to stay in California because of his son.
Garza patches up Nolan, telling him that she has read David Vincent's journal and has come to the same conclusions as Vincent. She says that Nolan has a "psychic ability" and he has to use it. Nolan persists in seeing subway-like visions as well as those of a man making a speech on a platform.
At the diner, Kyle confronts not only the bus passengers/aliens, but also his mother, asking her if she has an alien baby in her stomach. When Jerry tries to intervene, Kyle runs away.
Coyle gets romantically involved with Grace, and they "do it."
Kyle is living in an abandoned car in the desert near the diner. The cops visit Amanda and Jerry and insist that Kyle will come home soon.
Garza calls the diner and asks to speak to Carlos on the pretext of being Carlos's niece. Both she and Nolan tell Carlos that Kyle is in danger, and Nolan gives Carlos some hints as to where he thinks Kyle may be hiding out.
In a coffee shop, Nolan flashes on a newspaper with a story about Senator Alex Feinman (Jon Cypher), an aspiring political candidate with presidential ambitions. Feinman is on the ecology bandwagon, and is to be soon participating in a ceremony connected with the Los Angeles rapid transit system. Garza and Nolan are almost nabbed the cops, and they make their escape on a city bus.
Garza calls Coyle, saying that she believes Nolan and tells Coyle to read the journal, which is now in the cops' possession. Coyle takes her advice, reads the journal and goes to Vincent's house where he also sees the newspaper clipping of Nolan. Becoming more sympathetic to Nolan's cause, he tells his superior his feelings but is told to keep them low-key to avoid embarrassing the department (his superior smokes, so he is probably an alien).
At the diner, Amanda is feeling ill because of all the smoke from the bus passengers. Later, she snoops in the garage like Kyle, and sees Jerry inhaling carbon monoxide. Kyle returns and looks in Jerry's desk where he finds a schedule for the Los Angeles Metrolink. He also finds a probe device. He is seen by Jerry, who does not reveal his presence.
Carlos tracks down Kyle in the desert, but Jerry follows him and is about to shoot Kyle when Amanda blasts Jerry with a shotgun. Amanda tells Kyle to go to the city to see his father with the help of Carlos, then commits suicide rather than bear Jerry's alien child.
Coyle and Grace get involved in some kinky sex games. However, it's not what Coyle is expecting, since Grace gives Coyle the "probe" along with the octopus face monster.
Carlos and Kyle arrive in Los Angeles. They call David Vincent's house, where Nolan and Garza are presumably staying, but there is no one there. They decide to go Union Station where Feinman is giving his speech.
The Invaders turn off the methane detectors in the subway system. Nolan and Garza witness increased security on the subway platform. Nolan steals a security badge which enables him to contact Whitley (Jon Polito, uncredited!), a dispatcher in the subway operations centre to warn him about the increase in methane, but Whitley insists nothing is wrong. After seeing three security guards, one of whom he knows to be an alien, Nolan calls Whitley again and insists that they run checks on the air levels.
Nolan and Garza approach Coyle, who has joined the crowd for Feinman's speech, not knowing that he has been transformed into an alien. Coyle draws his gun, but Nolan escapes (again).
Whitley determines that there is indeed a problem with the methane levels, but it is too late to stop Feinman's trip on the train. Nolan has stolen a maintenance worker's uniform, and manages to sneak on to the train just as it leaves the station.
On the train, Coyle, who is programmed to make sure that Feinman dies, shoots the motorman and also Feinman's bodyguard. Nolan manages to sneak close to where they are, and with the help of Feinman's female assistant, manages to disable Coyle, who is then handcuffed to bars inside the subway car.
The train's brakes are disabled, and only after following instructions from Whitley is Nolan able to stop the train just in the nick of time before it runs into the end of the line.
Nolan, Feinman, and the assistant manage to escape up to the street at the station. Grace appears out of nowhere on the subway platform wearing a mini-skirt, and Coyle shoots her dead, which causes an explosion.
In the confusion, Garza, Nolan, Carlos and Kyle get away, and are seen at the end of the film driving up the Los Angeles aquaduct in a beat-up pickup truck.