Again Mr. Smith tells the children to run but they stand their ground. Tybo threatens to use his gun to destroy the computer before it can detonate, but instead Luke takes centre stage, reasoning with Mr. Smith that since his central protocol is to defend the Earth, and since Sarah's order contradicts this, he must therefore override the command to detonate. After considering this Mr. Smith accepts and cancels the countdown with one second left to spare.
At Genetec Systems Sarah (alias Androvax in disguise) manages to upgrade the nanoforms to widen their capabilities and forces Mr. Yorke to input their activation code. As he does so she reveals her plan for the microscopic droids - they are going to build her a spaceship.
Mr. Smith reveals what Sarah was looking for when she came to see him - she has gained access to the blueprints of the spaceship that crash-landed on Earth in 1947 in Roswell. Luke realises that Androvax plans to rebuild the ship and escape the planet before the Judoon fleet arrives - after being awakened from their sub-zero state of storage; the nanos will be able to construct the ship in less than thirty minutes.
At the lab Mr. Yorke realises that Sarah has reprogrammed the nanoforms to multiply at an accelerated pace, causing them to spill out of the containers and into the open air. He warns that they will devour the planet if not contained but this is all part of Androvax's plan - once the spaceship is constructed he will be able to cover his tracks by destroying Earth.
Meanwhile, Gita and Haresh are still being held by the security guard in his office. When a security alert goes up he is forced to leave them but locks them in to prevent them from causing any more trouble. Once he is gone Haresh begins trying to pick the lock, but with little success. Gita manages to save them time by locating a spare set of keys in the desk drawer.
Luke, Rani, Clyde and Tybo arrive outside the laboratory in time to find the nanoforms swarming on the roof of the building, beginning construction of the ship. Their arrival is detected by Sarah in the main lab, and despite her reflection - which shows the true Sarah hidden beneath Androvax's possession - warning her that they will stop the evil plan; she vows that they will never gain entry to the locked-down building.
Back outside, after Tybo forces them to adhere to the pay and display restrictions in the car park, Clyde, Rani and Luke try to get past the main door. Finding it locked Tybo draws his gun, but before he can fire Mr. Yorke manages to reverse the lockdown and allow them access. As punishment Androvax turns on Yorke and sends him into a paralytic trance.
Downstairs Tybo manages to scare off the security guards in time for his human aides to study a map of the building and head towards the laboratories. On the way Rani spots her parents walking around the facility and does her best to hide herself, her friends and their Judoon guardian.
Gita and Haresh, having gotten themselves lost, are looking for an exit when a squadron of four Judoon officers teleport into the building beside them. As Tybo did with Sarah, one of the troop scans the humans and adopts their language before leading the others away to carry out their tasks, warning that obstruction will result in death.
In the lab Androvax again quarrels with his reflection, belittling the suppressed Sarah for attempting to act as conscience. He threatens to harm her friends if she is not silent, but Sarah remains confident that he will not succeed.
Despite Tybo protesting that they are not authorised to enter the labs, Clyde, Luke and Rani make their way into the test rooms to search for Sarah. The room they try is empty but they do manage to trap Tybo - who has received communication from the recently-arrived troop - in a electro-dampening cupboard to stop him from slowing down their investigation any further and so that the other Judoon will have to find him first before they can look for Androvax, as his radio will not work in the dampening field.
Gita and Haresh watch as the Judoon search the building. It then dawns on Gita that the security guard took her mobile phone when they were caught, and drags her husband away to find it for fear of it, and all of her contacts, being lost.
Luke, Rani and Clyde manage to find Sarah and warn the creature possessing her that the Judoon have started to arrive in the building so he had better leave. Luke tells him to release his mother before he goes, but Androvax claims that he cannot, for he knows that once released, Sarah will not allow him to escape.
The children urge Sarah to fight the being controlling her, claiming she is strong enough to expel Androvax. For a moment it appears to work and Luke embraces her, but this is simply a trap to get him close enough to send him into a trance. This done, she turns on Rani and Clyde and, using the Sonic Lipstick as a remote control, summons a swarm of nanoforms to devour them. They run out of the lab and through the building, the black swarm spreading after them. Narrowly avoiding the Judoon squadron, they lock themselves in another laboratory.
In the main lab Sarah brings Luke out of his trance and takes him to the completed ship. Once inside Luke marvels at the scale of the nanoforms' construction.
Clyde and Rani search for a weapon to fight the approaching swarm and seem to find an answer when they recall Luke's claim that the nanoforms fall dormant in sub-zero temperatures. As the Judoon patrol manages to locate Captain Tybo and release him from the dampening chamber, they grab two fire extinguishers and freeze the swarm and hurry outside to find a way of stopping the robots for good.
Inside the spaceship, Luke urges Androvax to let Sarah go, but he refuses. Through his conversation it becomes evident that Sarah is fighting for control, her voice breaking through occasionally to reveal that Androvax's penchant for destroying other people's worlds was born from the destruction of his own. He admits that his planet was frozen by a dying sun, leaving his people entombed forever and him alone in the universe. His jealousy drove him to show other races the single truth of the universe: destruction.
Clyde and Rani continue their flight but find themselves in the company of Tybo and the other Judoon. Found guilty of multiple offences, they are sentenced to death but before Tybo can fire at them, the nanoforms turn on the building and begin devouring it, causing a tremor that acts as enough of a distraction to allow the two humans to escape. The Judoon follow.
They ascend to the spaceship - having been allowed in by Luke, who recalls all of the controls from the blueprints displayed by Mr. Smith, and watch as the young genius reveals that he has removed a vital fusion mechanism from the ship, rendering it useless. He warns that Androvax can only have it back if he releases Sarah and disables the nanoforms. Having seen the Judoon approaching, the volatile alien is forced to obey. He steps out of Sarah's body just as the Judoon arrive.
The tremors grow fiercer as Androvax reiterates to Luke that the only truth of the universe is destruction. He agrees that demolition is key to evolution, but claims that really the truth of the universe, it's once constant, is survival. He turns away and sets to work at the computer, using it to hack into the Genetec computer system and access the nanoforms' programming. He succeeds, and the swarm surrounding the building are deactivated.
Defeated, Androvax turns on Sarah and warns that, even if not by his own hand, one day she will be destroyed. He is led away by the four Judoon guards whilst Tybo turns to Clyde, Luke and Rani and claims that, having helped secure his prisoner they no longer face the death penalty, rather they are to be grounded henceforth to Earth. He then claims that the Judoon will confiscate the newly-built ship and orders the others to leave.
The four friends make their way outside, narrowly avoiding being seen by Gita and Haresh, and speed away in Sarah's car just as Mr. Yorke awakens and steps out side in time to see the ship take off and blast into the heavens.
Returning home, Sarah claims that although things may die all the time in the universe, just as Androvax claimed, that death is always the start of something new, and that is the stunning thing about the cosmos.
Soon they are joined by Gita and Haresh, who claim that they have seen aliens. Gita urges Sarah to turn their story into an article, and hurries away to prepare to reveal all, whilst Clyde joshes his headmaster about believing in the otherworldly. Mr. Chandra claims that nobody will believe the tale, claiming that to the rest of the world, Bannerman Road is an ordinary place - what could ever happen there? Sarah tells Luke:
"Oh, that's the wonderful thing about the universe.you just never know."