After discovering a plastic sphere labeled AAA/RH/2961 deep in the bowels of the Warehouse, Professor Sally Arnold has had Archivist Graham Winslet scouring the building looking for more crates with the same serial number.

Meanwhile Dr. Sal and her assistant Janice have been trying to figure out exactly what the sphere is. So far it has resisted all other forms of examination, but Sal is about to try and scan it with a satellite hook up. Before she can do so, she is interrupted by a call from Winslet who has found some crates with the same serial number with the letters A-U-T-O-N written on them. Not wanting to miss her window of opportunity, she puts him off. Soon after making the link up, the sphere begins to pulse with energy. Winslet has been trying to open one of the crates without much success. Just as he’s about to give up and leave, he hears a faint thumping noise from within. Sal notices on her computer screen that the sphere is communicating with something in deep space. When she tries to sever the connection, the sphere apparently explodes, killing Janice. Simultaneously, a fist bursts through the crate, Winslet is examining.

Believing an alien contagion may have been released, Sal calls in the Containment Team. All non-essential personnel are evacuated with the exception of Winslet and herself. When the Containment Team soldiers arrive, Sal and Winslet are clad in decontamination suits wondering if the rumors about Containment Teams are true. The soldiers burst in and shout “Freeze”. Thinking this is it; Sal apologizes to Winslet for saying he had bad breath.

Lockwood, the cold, cynical, telepathic team leader, arrives with his heavily bespectacled assistant Dr. Dan Matthews and is quickly debriefed by the ruthlessly efficient Sergeant James Ramsay. Lockwood and Dan first go to examine the laboratory where the sphere apparently exploded. Lockwood then asks Ramsay to bring Arnold and Winslet to him for questioning.

When he meets Winslet, he wonders why this non-essential personnel wasn’t evacuated. Winslet claims he wasn’t fast enough. Lockwood dismisses Winslet then begins to question Sally. “She’s in shock,” Lockwood says unsympathetically then leaves. Dan offers Sal a sympathetic shoulder to cry on when the emotional strain becomes too much to bear. Lockwood goes to question Winslet in the archivist’s office. He finds it hard to believe that such a meticulous, thorough and fastidious person like Winslet couldn’t make it to the safe house in time.

Sally, after changing in her room, has flashbacks about Janice’s death. Dr. Matthews arrives and again offers his sympathies. Sal asks what is going on, but Dan politely puts her off and begins to question her about what happened in the lab. Sal defends her actions about using UNIT’s satellite system to scan the sphere because it had resisted all other means of testing. When she asks if they might be in danger, Dan reluctantly replies, “We might be”.

Lockwood is called away from his interrogation of Winslet to join Sal, Dan and Ramsay at the scene of a dead UNIT soldier. Dan deduces that he was killed in the same manner as Janice. Lockwood has Sal taken away when she starts asking questions, then begins discussing their situation with Dr. Matthews. They don’t have the right equipment. They came expecting alien contamination, not a bug hunt.

Dr. Arnold is kept with Winslet in his office, impatiently waiting for what will happen next. Sal complains about Lockwood being high handed to a pensive Winslet. Ramsay is sent to bring Sal to the lab where Lockwood is waiting for her. (On the way she barrages Ramsay with questions to which he simply answers, “Yes, Doctor”).

Meanwhile, the sphere liquefies itself and oozes through the grill of Winslet’s office and reforms itself in is hand. Pulsing with energy, the sphere is absorbed into Winslet’s. A blank look on his face, Winslet raises his arm and his hand drops away revealing his true nature: he is an Auton. Humming tunelessly, he sets out to complete his mission.

Back at the lab, Lockwood viciously berates Sal for messing around with technology she doesn’t understand (“God save us from mavericks!”). Sal defends herself by pointing out that she has nothing else to work with. She was working with the best information she had (which isn’t much considering how little they’re funded). Lockwood offers no sympathy but Sal gives as good as she gets.

Ramsay and Dan find one of the Auton crates in storage bay one, and inform Lockwood.

Lockwood finally decides to tell Sal that they are dealing with the Nestene Consciousness and their lethal servants, the Autons.

Lockwood and Sal meet up with Ramsay and Dan to find a hidden vault. Ramsay calls for back up while Lockwood opens the vault hoping to find a way of defeating what it is they are up against. Ramsay and two soldiers take up a defensive position in front of the door while Lockwood, Sal and Dan go in. Inside they find relics from the first Auton invasion: the tank containing the remains of a Nestene, a second control sphere and the device used to defeat the Nestenes. They’ve done all this under the watchful observation of ‘Winslet’. He tries to activate one of the other Autons, but isn’t strong enough.

The second control sphere begins to pulsate and the other Autons come to life. Fighting breaks out between the UNIT forces and the Autons. While Ramsay and Dan try to hold them off, Sal and Lockwood flee back to the laboratory to try and figure out exactly how “Dr. John Smith’s” device works.

Dan and Ramsay are cut off from Sal and Lockwood, and find a comatose Winslet. They meet up with other soldiers only to discover all the exits are cut off. Dan is wounded, so Ramsay hustles him into a storage cupboard. The UNIT troops fight valiantly, but are inevitably picked off by the near indestructible Autons.

Lockwood mediates while Sal tries to figure out what the device does. Dan and Ramsay try to figure out what to do next. ‘Winslet’ tricks Sal into letting him into the barricaded storage room then takes both her and Lockwood back to the vault. Dan and Ramsay witness this and follow them.

When they reach the vault, ‘Winslet’ forces Lockwood to open it. It senses that Lockwood is connected to - something … He manages to resist long enough to tell Sal to work on the device. That and the timely intervention of Dan and Ramsay allow her to escape. An Auton chases them back to the storage room, but by them Sal has the device working and manages to deactivate it.

‘Winslet’ reaches into the tank and absorbs some of the remains of the Nestene. Lockwood throws off the Nestene influence long enough to stumble out of the vault. ‘Winslet’ follows telling him it’s only a matter of time before he succumbs to the Nestene Consciousness. Dr. Arnold arrives and destroys the Autons on guard then turns the device on to “Winslet’. It retreats into the vault. Lockwood stops her from going after saying it’s too dangerous. They call for back up and let the experts deal with this. It reverts to a gelatinous state, freeing the real Winslet, and escaping through the air ducts. Lockwood tells Ramsay to call for back up, knowing that it won’t due any good.

A few hours later, Sgt. Ramsay reports that they’ve combed the area up to a fifteen-mile radius and found nothing. Lockwood thanks Ramsay and tell him there’s nothing more he can do (“You’re a good chap Ramsay. I used to think your sort only existed in black and whit war films.”). A patched up Dan Matthews informs Lockwood that they found particle traces of the Nestene creature in the air ducts. It’s out there, somewhere.

Sal is packing, getting ready for debriefing. Lockwood arrives to thank her for helping with this crisis and for saving his life. He’s also here to inform her that he’s had her transferred to his team (“I think I’m going to enjoy working with you - Dr. Sal.” “I don’t think I’m ready for you’re type of work.”)