As fumes engulf the Earth the Doctor struggles desperately to free Wilf. His efforts are trumped though, when Sylvia arrives with a fire axe and smashes the windscreen.
At the ATMOS factory Colonel Mace orders his men to seal off all doors to prevent the gas from getting inside. He returns to the mobile HQ where his technical staff tells him that ATMOS has been activated across the entire world. Meanwhile, Martha’s clone enters and begins accessing the NATO defence system.
At Donna’s house Sylvia leads the freed Wilf inside. Seconds later Private Ross arrives in a taxi (the only vehicles not fitted with ATMOS) and tells the Doctor to get inside. Despite Sylvia’s protests Donna also goes with them, and finds support in Wilf, who realises she will be safer with the Doctor.
Back at UNIT mobile HQ Clone Martha downloads NATO security protocols onto a data chip and loads it onto a mobile phone. The codes are transmitted up to the Sontaran battleship, where General Staal orders that she must be protected from being discovered. Commander Skorr agrees to launch an attack squad in the factory and leaves. General Staal then turns to Luke, who is rejoicing in the destruction on the planet far below.
Whilst news reports warn the public to stay away from the poisonous gas, the Doctor, Donna and Ross return to the ATMOS factory. Inside the mobile HQ Clone Martha delivers the Doctor’s previous instructions to Colonel Mace and warns him that they are facing a threat from the Sontarans, a race UNIT has encountered before. Outside the Doctor tells Donna to return to the TARDIS where she will be safe, and hands her a key to the ship. He then hurries back inside.
He arrives in the mobile HQ and warns Colonel Mace not to engage the Sontarans in battle because the human troops will be slaughtered. He tells him that he will use the TARDIS to go onboard the Sontaran ship and prepares to leave, seemingly unaware that Clone Martha has sent a signal to the two conditioned UNIT soldiers waiting outside.
As the impostor companion leaves with the Doctor the two soldiers approach the nearby TARDIS and attach two alien devices to its doors. The Sontarans activate the pieces of equipment and the ship is teleported onto the battleship, with Donna still inside. General Staal examines the machine and is jubilant it is now his. Luke Rattigan, meanwhile, returns to Earth to summon his student and ready themselves for battle.
The Doctor and Clone Martha arrive in the alleyway where the TARDIS was taken and the Time Lord realise sit must have been taken by the Sontarans. He begins to question his companion; surprised she has not mentioned any concern for her family. She bluffs her way out of the situation and then returns with the Doctor to the ATMOS factory.
The students of the Rattigan academy watch as London is engulfed in fog. Luke arrives and tells them that they must not concern themselves with it because they must concentrate on their work.
Returning to HQ the Doctor listens as the first reports of death from the fumes are sent in. Meanwhile Colonel Mace has been preparing to fire NATO nuclear strike at the Sontaran ship, which has been detected orbiting the Earth. The Doctor warns him such an attack will have no effect on Sontaran defences and instead opts to talk to the creatures himself.
He establishes a visual link with the battleship, which is overseen by Donna in the TARDIS via the scanner. However, unbeknownst to Donna that is not the only signal reaching the ship. Before the image of the Doctor appears the face of a girl screaming for help is seen amidst the interference on screen – it is Rose.
The Doctor turns on General Staal, calling him a coward for using poisonous gas instead of confronting the humans face-to-face in battle, as would befit a Sontaran. He theorises that instead they must be planning something else; this is not usual Sontaran behaviour. He questions whether it is a strategic move in the Sontaran’s war with the Rutans, which he suggests may be going badly for the aforementioned side. Staal rubbishes this claim and leads his men in a victory chant, which the Doctor ignores. His attention is gained, however, when Staal reveals the TARDIS is onboard his ship.
The Doctor manages to speak with Donna without arousing suspicion from Staal, and tells her to call him on the mobile phone he keeps on the console. She finds the device but doesn’t know what number to call. Meanwhile Staal severs the communications link when the Doctor threatens to regain the TARDIS using the Sonic Screwdriver as a remote control device. The ship is moved out of the main war room, instead being placed in a section of the ship where the transmission field from Earth will not reach it.
At the Rattigan Academy Luke tells his students that the experiments they have been conducting are preparations to be used to create a new world for them to live on. The Sontarans have promised to take Luke and his students to a new world where they can create a new superior human race, away from the scorn of people who belittled their intelligence. However, the young scientists do not believe in his plans, for they are more concerned with the well being of their families. They desert him, and he is left in a fit of rage.
The toxic fumes continue to spread and the population descends into panic. Thousands of people begin fleeing into the open countryside whilst others are seeking refuge at sea.
In the TARDIS Donna calls her mother and tries to reassure her that she is safe and everything will be all right. Wilf takes the phone and speaks to his granddaughter, concerned that she is safe from the fumes. He is disgruntled that the Doctor is not with her but seems assured when Donna promises that wherever he is, he will be able to save them all.
At UNIT mobile HQ Clone Martha has analysed a sample of the gas and shows the report to the Doctor. He notes that there is an unidentified element in the chemical composition, and that it is the rogue element that the Sontarans need. He believes the gas is not just poison; it is something else as well…
Colonel Mace begins to launch the nuclear strike and the Doctor is distraught. As each nuclear station across the world goes online General Stall looks on from the Sontaran battleship, claiming, “the bravery of idiots is bravery nonetheless”. Commander Skorr claims their operative working within UNIT will be able to stop the attack, and then assures his General that the Sontaran Attack Squad is ready.
As the countdown to nuclear strike reaches zero Clone Martha is able to stop the missiles using the protocols she has downloaded. The Doctor comments that the strike wouldn’t dent the battleship yet the Sontarans are keen to stop the attack. He turns to Martha for an explanation but she has none.
Soon the Sontarans are beginning to swarm the lower levels of the factory, with the objective of collecting the Clone of Martha. Private Ross and his men hear the troops approaching and prepare to defend themselves, but their weapons are rendered useless by the alien signal being transmitted by the Sontarans that causes the bullets to lodge in the barrels of the guns. Ross contacts Colonel Mace to warn him of the attack and the base goes into red alert. He and his men are gunned down, and the Sontarans advance.
The Doctor orders Colonel Mace to withdraw his men and he complies, ordering a full retreat. However, battle has already begun as the Sontarans storm the factory. The two conditioned guards are gunned down in the process as the UNIT soldiers are massacred, just as the Doctor predicted. The Time Lord wonders why the factory is so important to the Sontarans and wishes he had the Brigadier with him to help. Colonel Mace apologises, claiming Sir Alistair is stranded in Peru.
Another nuclear strike is prepared but again Clone Martha manages to thwart it. Colonel Mace order the source of the sabotage is found, whilst outside the toxicity of the gas increases.
Luke returns to the Sontaran battleship, claiming he has failed in his mission to gather the population of his new planet. General Staal seems nonplussed by this, and admits that it doesn’t matter; the students were to be used as target practise in any instance. Luke is confused by this and listens as Staal explains that the promise of a new world for Luke was simply a ploy to secure his cooperation – he was needed simply to install the ATMOS system – nothing more. Luke grows infuriated by this but evades being shot down by teleporting away. Staal brands him a coward and then orders for all teleport links with the ship to be closed. Back on Earth Luke is left alone in his Academy, reduced to tears.
At UNIT mobile HQ the Doctor continues to wander what it is that the Sontarans need inside the factory. As Colonel Mace continues in vain to try and fight back the Doctor takes Martha’s phone and calls Donna. He explains that he needs her to reopen the teleport link, which he has assumed will be closed down now the creatures are at battle stations.
Reluctantly she agrees and slowly opens the TARDIS door, only to find a Sontaran standing guard outside. The Doctor tells her to hit the creature on its probic vent, which she does so using a hammer sitting beside the ship’s console. She progresses down a corridor and the Doctor tells her to find the teleport controls. He guides her along but is forced to abandon her when Colonel Mace arrives. He hands the Doctor and Clone Martha gas masks, and they follow him outside.
Meanwhile, on the Sontaran ship, Donna takes cover as a troop of soldiers pass her in the corridor. She sits and waits for them to pass; terrified that she might be seen.
Colonel Mace shows the Doctor a new supply of ammunition which should be unaffected by the Sontaran’s crippling signal. The Doctor is still sceptical and notes that battle will be useless in the fog – they cannot see the enemy. Mace ignores him and instead rallies his troops to fight back. Seconds later a strong wind picks up and the fog begins to clear. The Doctor looks up into the skies and sees a familiar shape – the Valiant. Now a UNIT carrier ship the craft’s engines are powerful enough to sweep away the gas, leaving the air clear.
Mace then orders the ship to fire upon the factory. A lightening green laser shoots from the ship and hits the complex, demolishing the Sontaran forces inside. Soon the UNIT soldiers are putting up a palpable defence and the troops begin to swarm the building. The Doctor and Clone Martha hurry inside, the Time Lord taking a moment to assure Donna via the phone that he is still with her. He begins scanning for alien technology and heads towards the basement. Martha is in quick succession, pausing only to stop another nuclear attack.
Eventually the duo arrives inside the chamber where Martha was cloned. The Doctor discovers the real Martha still strapped to the operating table, and runs to help her. He confesses that the clone of his friend did not convince him but he found her useful for stopping the nuclear strikes. He realises that the reason the Sontarans protected the factory was to stop the real Martha from being discovered – whilst she is unconscious the clone can survive.
He disconnects Martha from the Sontaran equipment and immediately her clone topples over in agony. The Doctor helps Martha as he reawakens then answers a call from Donna, who has found the teleport controls on the Sontaran ship.
Whilst Colonel Mace dispatches Commander Skorr up above, in the basement the Doctor tries to repair the teleport unit and Martha confronts her duplicate. She tries to ascertain what the Sontarans are using the gas outside for and she recites the unknown part of the toxin’s chemical composition. The Doctor recognises the new element as clone feed, and realises that the Sontarans are going to use Earth as a clone planet. They have no need to invade because soon new warriors will be born all over the planet.
The beat of Clone Martha’s heart begins to slow, and the real Martha is only able to look on as her duplicate dies. She takes the wedding ring from the clone’s finger and places it on her own.
Donna calls the Doctor and tells him she has completed her work, but the Sontarans have found her. They aim their weapons at her but before they can fire the Doctor manages to bring her back to Earth. He then sends the TARDIS back to the alleyway and ushers Donna and Martha inside the teleport pod. He activates the device and they arrive at the Rattigan Academy, where the distraught Luke is still alone.
On the Sontaran ship General Staal orders the ATMOS devices to be set to maximum conversion, and across the globe the fog gets thicker. At Donna’s home Wilf and Sylvia find themselves at the mercy of the gas, which is seeping into the house. Sylvia breaks down in tears and Wilf comforts her, reminding her that Donna promised they would all be saved.
At the Academy the Doctor rushes around trying to construct one of the experiments Luke’s students were working on. He explains to the others that the Sontarans were holding back the nuclear strikes because the missiles would ignite the atmosphere and burn away the gas. Now he intends to finish the job only by a more humane means – by using an atmospheric converter made by the students.
General Staal prepares to launch the clone pods that shall soon inhabit the Earth whilst on the planet below the Doctor runs outside and activates the atmospheric converter. A bolt of light fires up into the sky and ignites the poisonous fumes. Soon a blanket of fire is sweeping across the city. Staal can only look on in vain as the purifying flames spread across the Earth, leaving the air breathable once more. The UNIT troops and the people of the Earth rejoice, just as Donna promised, they have been saved.
However, the Doctor claims there is still trouble to come, and he is right. On the battleship General Staal orders his army to prepare for an invasion – the Sontarans cannot accept defeat and so therefore they shall wipe out the human race as compensation for failing to create a new breeding planet.
The Doctor hurries inside the Academy ad steps inside the teleport pod. He says goodbye to Martha and Donna and then tells Luke to do something clever with his life. Martha asks why he is saying farewell and he explains that he must stop the Sontarans – which he will achieve by destroying their ship with the recalibrated atmospheric converter. Martha asks why he cannot send the device on its own and set it on a timed delay, and he tells her it is because he must offer the Sontarans the option of surrender.
He teleports away and arrives on the ship, where he tells General Staal that if the Sontarans leave he will not activate the device and destroy him. Staal tells him the Sontarans do not fear death, and his warriors aim their guns at the Doctor. As the battleship prepares to open fire on the Earth the Doctor hesitates, but his choice is made for him when Luke reactivates the teleport.
He sends the Doctor back to Earth and takes control of the atmospheric converter’s controls. With a mocking recitation of the Sontaran battle cry he activates the device and the Sontaran battleship is destroyed in a colossal explosion.
The city of London returns to normal, only now the public are somewhat reluctant to use their cars. Donna returns home again to see her family, and once more Wilf warns that her mother must not know of her travels with the Doctor. He tells he she must go with the Time Lord again and see the stars, and tearfully she says goodbye to him.
Eventually she returns to the TARDIS, where the Doctor and Martha are waiting for her. She asks Martha is she going to join them on their next journey but she declines the offer; although she has missed her time with the Doctor she has a whole new life to explore on Earth.
She is about to leave when the ship doors slam shut and the console begins to set the craft in motion. The three travellers are left at the mercy of the machine, which appears to be piloting itself. As the jar containing the Doctor’s severed hand begins to bubble and glow Martha orders the Doctor to take her home…