UNIT is covertly moving the Autons for further study in an unmarked trucked manned by two operatives, Mike and Dave. Late at night, they come across a roadblock. When Mike tries to call for instructions all he gets his static. Mike goes out to investigate only to find no real reason for the obstruction. He finds the Nestene energy unit that escaped from the Warehouse two years previously. It revives the Autons, who kill Dave and Mike then drive off in the truck. UNIT’s special operative, Lockwood, apparently witnesses all this in a dream.
At Containment HQ the next morning, the man in charge of the operation, Colonel Wilson informs Lockwood of last night’s incident. Naturally enough, Lockwood is far from impressed with the rigid colonel when he tries to wax over the fact that he has lost a bunch of alien killing machines. Sally Arnold his brought in on the meeting and is shocked to learn that the Auton dummies weren’t incinerated two years ago after they spent six months dissecting one. Sal and Lockwood return to their separate quarters to get dressed before continuing their interview with Col. Wilson. Lockwood seems to have a psychic vision of the Auton’s drive to the seaside then vaporize the truck and walk into the sea. On their way back to the briefing room they discuss whether or not the control unit was behind it. Wilson shows them a release form that shows it was Lockwood who authorized the Autons relocation. Colonel Wilson then informs Lockwood that he has been ordered to aid Wilson’s team in their investigation of the missing Autons. Lockwood resents his team being left out and demands that Dr. Arnold accompany him. Wilson denies his request and leaves’ telling him the car is waiting for him outside. After the officious colonel leaves, Lockwood and Sal agree to keep in touch.
Meanwhile on Sentinel Island, Daron, the church gardener, believes he hears the voice of God telling him to meet His disciples. Daron races to meet the coming disciples. He meets the escaped Autons in the middle of a field and his overwhelmed by a total sense of rapture.
Lockwood arrives at the scene of the disappearance and is pleased to find a friendly face in the form of Sergeant James Ramsay. Sgt. Ramsay is equally pleased to see Lockwood and asks about Dr. Arnold and Dr. Matthews. Lockwood tells him that Dan is in Africa digging up alien artifacts and Sal in back at Containment HQ (“Apparently my team isn’t good enough”). Lockwood meets Wilson’s scientific advisor, a young psychic woman called Natasha Alexander, and is far from impressed. They both get a feeling from a sheet found at the site. Lockwood contacts Sal and scans the sheet. Sal receives the readings and confirms that the Nestene energy unit was there. It was the sheet the control unit was wrapped in. Somebody put the sphere here to be found, but who? Lockwood has a piece of the sheet sent to Containment HQ for analysis then, uncomfortable around Natasha, goes to wait in the car. In the car Lockwood call Sal to tell her he’s sending her the sample and to ask her to look up Natasha Alexander in UNIT’s database. Sal can’t find her in the standard personnel manifest so she’s obviously important. She then gives him the results of her analysis of the sheet. In private, Col. Wilson asks Natasha if she can work with Lockwood. She can but knows he won’t make it easy. Lockwood gives Col. Wilson the results of where the sheet was manufactured within a hundred mile radius. The colonel complains that this is going to require an increase in man-power and just because the sheet was made doesn’t mean that’s where they’re going. As far as Lockwood’s concerned this doesn’t concern him and more than anything, Wilson need to start somewhere.
The people of Sentinel Island welcome the Autons with applauds. Like Daron they are all experiencing the rapture. The new vicar (who looks a like Senior Archivist Winslet) has been whipping the people into a religious frenzy with Daron’s help, making it easier to bring them all under the control of the Nestenes. But there are some people who are able to resist the Nestenes influence. The vicar uses Daron to identify them. The resistors are ruthlessly hunted down and killed by the Autons.
Back in the car, Natasha tries to get Lockwood to open up. UNIT took her in when she was a child. Her parents didn’t want her (they couldn’t lie to her and she blew all the fuses in the house when she was smacked and sent to her room). Lockwood remains stoicly silent, not showing any interest in her history. She then shows Lockwood a map and tells him to point to where he was thinking when he touched the sheet. He denies he was thinking anything but she knows better and pushes the issue. He takes the map and point to Sentinel Island.
All the people resistant to Nestene control have been killed except one, Daron girlfriend Charlotte. Daron pleads with the vicar to spare her life and that he can convince her to come around. Daron turns Charlotte over to the Autons and brings her to the church where the Nestene energy unit is sitting on the pew, pulsing with energy. She tries to resist but his eventually taken over like the rest of the villagers.
The UNIT soldiers prepare to land on Sentinel Island. Col. Wilson still isn’t convinced that Autons are here, despite Natasha’s reassurances. Lockwood calls Sal for information on the island and an update on her research. He believes that the creature from the Warehouse is on the Island. Sal tells Lockwood that Natasha works for the Internal Security Division and wonders why they’re investigating him. When she mentions that the island is on a lay line his face goes blank. He remembers that he did in fact authorize the transport of the Autons.
As the UNIT team prepare to land on the island, the church is flooded with psychic energy. Natasha and Lockwood sense they are being watched and Wilson sends Ramsay and Private Hardgraves to scout ahead. The vicar detects the arrival of the soldiers and orders the Autons watching them to keep them from interfering. Lockwood’s mind briefly connects with the control sphere. Now the Nestene’s know ‘UNIT’s creature is here. The Autons attack. Hardgraves is killed and Ramsay informs Col. Wilson. The battle for Sentinel Island has begun.
The fight with the soldiers has weakend its hold over Charlotte. She manages to shake off the Nestene influence. Daron tries to stop her but she escapes. Charlotte flees through the village and Daron goes after her. The vicar tries to stop him but Daron goes after her anyway. Daron makes it to the edge of the church yard before collapsing in total rapture.
The shoot out rages on, col. Wilson tries to call for back up only to get interference. Ramsay orders Private Davis to break out the AT-36. With the AT-36 they manage to destroy an Auton. But Lockwood knows this whole thing is just a distraction to keep the soldiers busy. He sees Charlotte and goes after her with Natasha and Ramsay in hot pursuit.
They manage to catch up with Charlotte but before they can question her she is shot by an Auton. Before she dies, she tells them there’s something under the church. Ramsay keeps the Auton at bay but knows they can’t stay here and their way back to the others is cut off so they make for the church. Lockwood finally confronts Natasha and demands to know why the ISD are investigating him. She reveals that UNIT thinks that the Nestenes may have gotten a foothold in his mind. She was sent here to see if that’s true. Ramsay is angry that UNIT thinks Lockwood could be a traitor, but Lockwood suggests they head for the church. Ramsay leads the way but Lockwood hang back long enough to tell Natasha that if he is working for the Nestenes, he doesn’t know it.
Halfway to the church, Lockwood sends Ramsay back to get col. Wilson and the rest of the men, despite the sergeant’s protests. Natasha finds Daron lying on the ground in a state of confused euphoria. The Autons capture them and the vicar arrives. The vicar informs Lockwood that he’s been betrayed by his own people then tells Natasha that Lockwood has finally found a place to belong.
Inside the church, Lockwood is told that the last time he encountered the Nestene control unit a special seed was planted in his mind and it has been growing ever since. Natasha asks what is under the church and it is Lockwood who answers, he is know connected to the Nestene intelligence. They are awakening a surviving Nestene creature, a beacon for the Nestene Consciousness. With Lockwood’s knowledge of UNIT’s plans for combating alien invasion, the Nestenes will be unstoppable. The church is flooded with Nestene psychic energy, even Natasha can’t fight it.
Feeling betrayed, Daron races back into the church and smashes the control shpere, destroying the Auton’s power source and releasing Lockwood and the others. Daron collapses. The villagers flee in panic while Lockwood staggers outside with Natasha’s help. But it too late, the creature is awake. It kills Daron as it smashes its way through the roof of the church and uses the steeple as an energy beam to contact the Nestene Consciousness. With Lockwood connected to it, they will know everything he knows, leaving the Earth open to invasion. Everyone will be killed except Lockwood, he will live on in the Consciousness.
Ramsay rejoins Wilson as he is nervously examining one of the deactivated Autons. With the Autons dead he can’t believe that Lockwood and Natasha are in any danger until he hears the creatures roar.
Natasha tries to convince Lockwood not to be taken in by the vicar’s promises of belonging, to look into her mind to see he isn’t alone on this world. Natasha is knocked out while trying to open his mind, but something happens. The whole island begins to shake, then the creature stops transmitting to the consciousness and vanishes. The vicar asks what Lockwood has done before it collapses, reverting to its natural Auton form. Natasha regains conscious and tells Lockwood she hasn’t finished with him yet.
On the boat back to the mainland, Natasha tells Lockwood she isn’t finished her investigation and realizes that the creature hasn’t gone. Exactly which side is Lockwood on?