The TARDIS materializes in the village of Lannet in Lancashire. An annoyed Doctor, who has apparently been transported here against his will, is locked out of the TARDIS and forced to examine his surroundings. After determining he is in England in 2003, he is surprised to discover the village is silent and the inhabitants all living in fear except for a barmaid named Alison Cheney. After the patrons and bar owner refuse to tell the Doctor what's going on, he leaves the bar and stumbles upon a lava statue and a homeless woman who is frightened. As the woman is beginning to fill in the Doctor on what's been happening, a tremor strikes the area and the woman is killed by a mysterious force. Back at the TARDIS, the ground opens up and the Doctor's police box is swallowed up into the lava below. Angered at the homeless woman's death, the Doctor tracks down Alison and her boyfriend Joe at their home and breaks in demanding that someone tell him what's been going on. Alison tells the Doctor that three weeks ago, strange noises began coming from underground. She has seen mysterious aliens around town watching her. The townspeople have convinced themselves that they need to stay indoors and make as little noise as possible. The Doctor begins making noise to attract the aliens, who burst up through the floor in a pool of lava. Immune to their shrieking cries, he deflects their noises back at them causing them to explode. The Doctor, Alison, and Joe flee next door where the Doctor explains that the aliens have bodies that can remake themselves. He improvises a large explosion which he believes will disable them and buy time. The explosion destroys the two alien worms and causes the noises from the ground to stop.
The Doctor contacts UNIT and explains that he is not interested in getting involved in this problem. He gives them all the information he has on the aliens and tells them that once he retrieves his TARDIS he is leaving. The aliens have begun nesting below ground at a site rich with a special volcanic rock the Doctor believes they have adapted themselves to use. He maps out the area and leads a UNIT team down into some caves to find his TARDIS. After a tense exchange with the UNIT commander, the worm creatures attack and the Doctor separates himself from the group and hitches a ride in a giant underground worm to the main lair of the aliens. There he meets Prime, commander of the Shalka. Prime declares humans inferior and subject to their domination. The Doctor attempts to act inept to extract information from Prime, who sees through the act and calls him out on it. Prime reveals that the Shalka are 2000 strong and will be invading the surface soon. The Doctor attempts another bluff, declaring himself a non-human and therefore uninterested in what happens to the humans. Prime orders Alison executed in hot lava, which forces the Doctor to make a deal to spare her life. He allows the Shalka into the TARDIS and de-activates the Master, who turns out to be an android programmed by the Doctor. The Shalka tell the Doctor his technology is inferior and they do not need him. He is cast into a black hole they have created inside Earth that they are using as a gateway to bring in more troops and also to dispose of people they do not need. As he is plummeting into the black hole the Doctor realizes his phone is still connected to the TARDIS and uses it to summon the TARDIS. He finds the Master re-activated and forcefully expels the Shalka from the TARDIS into the black hole. For an unknown reason, the Shalka release Alison back to the surface.
As UNIT evacuates the town, a soldier tells the Doctor he has captured one of the Shalka on the surface. The Shalka was accidentally exposed to raw oxygen when a cylinder near it exploded. The raw oxygen caused it to pass out. The Doctor also discovers that Alison is alive, and that none of the survivors from the town have made it to their new destinations. The Doctor attempts to interrogate the Shalka but it recovers and attacks the soldier. The Doctor uses more oxygen to subdue it until he can determine what's going on. He also discovers that the survivors all have sore throats. The survivors and Alison all march against their will to a warehouse in another town. The Doctor arrives in his TARDIS with UNIT men inside and they storm the area. The Doctor removes a living Shalka from Alison's forehead but the effort causes him to pass out. When he recovers they find that all around the world people are mobilizing against their will to strategic points on Earth. The Doctor realizes that the reason everyone has a sore throat is that they all have been emitting subsonic screams when under Shalka control. The Shalka are using the screams to alter the atmosphere of the Earth. As the slaves begin emitting their screams and the ozone layer of the Earth is being stripped away the Doctor takes Alison and the Master back to the Shalka underground lair. When asked if the Master is coming with them, the Doctor tells Alison that the Master cannot leave the TARDIS. The Doctor and Alison confront Prime, who tells them that the Shalka inhabit 80% of the worlds in the universe, living underground off of volcanic energy. When a species is on the edge of ecological destruction, the Shalka come in and finish destroying the planet. The rest of the universe assumes that the species that died off did the damage to themselves, and the Shalka live underground in the remains of that world.
The Doctor swallows the small piece of Shalka he removed from Alison's forehead. He bonds with it, reprogramming it to do what he wants. He uses its knowledge to plug himself into their sonic network and understand the shrieks. He engages Prime in a "sonic duel", which he purposely throws to get Prime to move him toward the black hole controls. He activates the black hole, sucking in Prime and sending her to her death. Alison stops the black hole and the Doctor coughs up the piece of Shalka. He puts it back in Alison's head, where she fights off the remaining Shalka and shuts down the screams. The Doctor unplugs her a few moments before she can reprogram the scream to heal the atmosphere. He tells her that she cannot be allowed that much power. On board the TARDIS, the Master reveals that it has been a long time since the Doctor had a living companion. His last companion was killed in the events that also led to the Master choosing to have his consciousness placed in the android and to the Doctor's exile. Without being specific, the Master tells her that they are being controlled by an unknown force and the Doctor wants Alison to stay as his companion but he won't ask her to. After they land, Joe arrives and Alison tells him she is leaving with the Doctor because she is bored and wants to see the universe. Joe reluctantly accepts her decision and a kiss before the Master begins the TARDIS dematerializing cycle and they board the craft.