Over time, the group of martians all learn of how they mistook the War of the Worlds radio dramatization for an invasion of Earth by their planet’s space armada, and later, they discover that their damaged ship’s hyperdrive is undergoing a meltdown, and if they don’t get back to zero gravity within an hour, it will implode and create a colossal black hole.
With help from their new human friends Wrenchmuller, Kathy, her father Sam, and her friend Brian, they get their ship to Wrenchmuller’s farm and put it into a vertical launch position, and Wrenchmuller sticks his entire stash of dynamite under it planning to have the explosion give them a huge boost up into the atmosphere, where they can reach gravitational escape velocity and get into space. The ship’s Enforcer Drone then appears ready to kill the martians for their invasion error, but Wrenchmuller pretends to be Earth’s ambassador and gives the Drone a lit stick of dynamite as an “award” for stopping the martians, which blows it to pieces.
Wrenchmuller detonates the dynamite and sends the ship skyward, but the martians have trouble reaching gravitational escape velocity. Thankfully, they achieve it after dumping the sewage tank to make the ship lighter, and the sewage rains down onto Wrenchmuller’s dead green bean field. The next day, Wrenchmuller finds that the sewage has caused his field to sprout six-foot-tall beans, giving him a crop to sign over to Klembecker and saving both his land and the town from Klembecker’s real estate development ambitions. In space, Captain Bipto suggests to his crew that they head to Arcturus to torture prisoners, but they tell him to shut up.
While trying to repair the ship in Wrenchmuller’s (Royal Dano) barn, Blaznee tunes into the local radio station and hears the station’s rebroadcast of Orson Welles’ War of the Worlds, and he quickly realizes that his planet’s space armada isn’t invading Earth. The Enforcer Drone which is programmed to kill the martians if they ever fall out of line then emerges from its garage and shoots Blaznee over the mistake before leaving to find and kill the others (however, it doesn’t notice that Blaznee isn’t dead). A short time later, Wrenchmuller and Deputy Russell (Fred Applegate) find the unconscious Blaznee, and they put him in Wrenchmuller’s truck and bring him to a town Halloween party to show everyone that martians are on Earth.
Blaznee awakes after they get there and runs into a nearby hiding place before the disbelieving townsfolk can see him, but Sheriff Sam (Douglas Barr) then arrives and backs up Wrenchmuller’s and Russell’s story, after having seen their ship captured on videotape from the video recorder in Russell’s patrol car. After seeing an old newspaper Wrenchmuller brought that shows near-precise illustrations of the martians, Mrs. Vanderspool (Patrika Darbo) confirms having seen them (specifically Giggywig, Pez, and Dr. Ziplock) with Sam’s daughter Kathy (Ariana Richards) earlier on, and she had told her that they were “her cousins from California” in costumes. Suddenly, the aforementioned martian trio announce their invasion of Earth to the people over their hovervid device, and to show that they mean business, they destroy the town’s new highway off-ramp and make popcorn out of a corn silo at the co-op (which they believed was a missile silo). This spurs the locals to get their firearms and find and kill them. Blaznee is found nearby by Kathy’s friend Brian (J.J. Anderson), who orders him to take him to his ship. Blaznee does so when he sees the Enforcer Drone approaching nearby, and Brian ends up helping Blaznee try to make it flight-worthy. Giggywig, Pez, and Ziplock then find the radio station that broadcasted the War of the Worlds and quickly realize the mistake they made.
Ziplock activates a homing beacon to bring the ship to them, starting up the ship’s auto-pilot and leaving Blaznee scrambling to try to override it. Vern (Wayne Alexander) having earlier been put under a mind control device by Captain Bipto and made into his robot slave drives Bipto from his garage to the beacon’s location, Kathy follows the martians’ Scout-in-a-Can robot she befriended to the location while trying to bring it to the barn, and the Enforcer Drone homes in on the signal. Wrenchmuller then returns to the barn and steps aboard the ship with a stick of dynamite planning to blow it up, and he throws Brian out of it. Blaznee traps him in a paralyzing beam, and the ship starts flying in small bursts away from the barn until it stops in the middle of a road. While chasing after the ship, Brian meets up with Sam and Russell as they are following the gun-toting townsfolk and tells them which way the ship went. Kathy and the Scout robot reach the ship and quickly get on it after spotting the Enforcer Drone approaching. Blaznee makes the ship take off again and knock the Drone senseless before landing on another road, where Giggywig, Pez, Ziplock, and Bipto show up and step aboard. The crew informs Bipto of the error they all made, and Blaznee points out that the Enforcer Drone is on the loose just as the townsfolk appear and start shooting at the ship. After Sam and Russell arrive and make them stop, the martians come out wrapped in a Donut of Destruction and tell them that they will blow up the Earth with it, but the device falls apart soon after they activate it. However, the smoke emitting from it enables them to slip away. Kathy gets out of the ship to get help for Wrenchmuller, who is now free of the beam, and the Scout robot escapes while the Enforcer Drone sneaks back aboard to wait for the martians to come back. Sam puts Russell in charge of watching the ship and keeping order among the people, and then drops off Brian at his home while taking Wrenchmuller, Kathy, and Vern back to his place.
Kathy tries to convince her father that the martians are not evil, just stupid, and that they want to leave Earth, and they might have a chance at that if he handled the situation himself instead of calling in some branch of the military to deal with them. Later on, the Scout robot finds and summons Kathy, Brian, and the martians to meet it at the co-op so they can all discuss a plan to get the ship back. When Sam notices that Kathy is missing, he takes off to find her, and Bipto contacts Vern and tells him that now is the time for them to unleash the “surprise” they have been working on for the invasion. As Vern leaves for his garage, Wrenchmuller overhears him going over the details of the “surprise” and follows him in secret.
Just then, Blaznee warns everyone that he has just discovered that the ship’s hyperdrive is having a meltdown, and it will implode and create a colossal black hole within the next hour if they don’t get the ship back into outer space before then. Kathy, Blaznee, and the Scout robot head back to the ship’s location and stay out of view of the townsfolk (where Kathy spots her father there), and the others go to Vern’s garage to meet up with Vern and get the “surprise.” The “surprise” turns out to be a “Farmzoid,” a large robot made out of farming machinery, and while they watch the end of its construction, Wrenchmuller reveals himself and says that he wants to help them now. The martians plan to have Vern drive it up to the townsfolk and distract them with it, which will allow Blaznee to get onto the ship unseen and fly it out of there. Sam finds Kathy and Blaznee, and they explain what will become of the ship in fifteen minutes from now and how a diversion will be coming to distract the people so Blaznee can get onto it. Vern then appears in the Farmzoid, and as the people focus on that, Kathy, Sam, and Blaznee get on board. Blaznee manages to get the ship to fly in short bursts, but it lacks the power to even get up high off the ground, let alone into outer space, so he radios this issue to Bipto. After getting confirmation from the martians that they can tip their ship up vertically, Wrenchmuller tells them that he has a solution back at his farm, so he has Bipto radio Blaznee and tell him to go there.
After everyone arrives there, the martians get their ship vertical, and Wrenchmuller puts his entire stash of dynamite under it, planning to boost it up into the atmosphere with the explosion, where they can reach gravitational escape velocity and get into space. As the preparations happen, Bipto lets Vern go free, but then the Enforcer Drone comes out and scares the martians out of the ship. Kathy and the martians explain to it what will happen if they don’t get the ship back into space, so the Drone allows the martians to get back aboard, but soon make it clear that they will be killed once they are back in space. Wrenchmuller then pretends to be the Ambassador of Earth and thanks the Drone for stopping the martians from causing more trouble than what has already taken place, and then gives it a lit stick of dynamite as an “award” for his heroism. The Drone is subsequently blown to pieces. Wrenchmuller then detonates the dynamite under the ship and sends it into the atmosphere, but the martians have trouble reaching gravitational escape velocity. They solve this problem by jettisoning the sewage tank to make the ship lighter, and as they go into space, the sewage rains down onto Wrenchmuller’s dead green bean field.
Klembecker (Gregg Berger) comes to the farm at noon the next day along with a none-too-thrilled Sam and Kathy ready to evict Wrenchmuller. Wrenchmuller tosses the house keys into the backyard and tells Klembecker to go get them, and after he goes, Wrenchmuller asks Sam and Kathy if they want to hear something funny in a few seconds. They then hear Klembecker scream, and they go out back and find that the martians’ sewage has caused Wrenchmuller’s field to sprout six-foot-tall beans, giving him a crop to sign over that will save not only his land, but will pay off all of the town’s loans and negate Klembecker’s real estate development ambitions. Meanwhile, as the martians are flying for elsewhere, Bipto suggests to his crew that they head to Arcturus to help torture prisoners, but they tell him to shut up.