The war between the Daleks and humanity has been raging for a hundred years and seems interminable.
The TARDIS lands in a petrified jungle, much to Amy's consternation. She asks which planet they are on but the Doctor says that they shouldn't be on a planet at all though he recognises the place and says that the devastation is the result of a nuclear fire that burned for a thousand years... they realise that the jungle is inside a very large room and locate a window that shows them a view of outer space.
A screaming man runs through the jungle, begging not to be left behind. He reaches a door but is denied access. By the time the Doctor reaches him the man is mutating into a Varga plant. The Doctor tells Amy not to touch him. A Slyther appears on the scene and kills the mutating man while the Doctor and Amy make their escape. The Doctor tells Amy that they appear to be on Skaro. The door opens and a group of armed and uniformed soldiers enter. The Doctor shows his psychic paper as identification while telling them that the man they are looking for, Hadleigh, is already dead. The soldiers take the Doctor to meet Tranter. On the way they pass a cell containing Robomen (who are permanently kept on suicide watch) and a cage full of Ogrons.
The Doctor is led into Commander Tranter's office and introduces himself as an inspector and Amy as his expert in 'stuff'. Tranter is annoyed that Earth Central doesn't trust him after he has been fighting on the front line against the Daleks for ten years. He says he has been in charge of Station 7 for a month since he was offered any desk job he liked. The Doctor says that he knew and worked with Bret Vyon and Sara Kingdom. Tranter is impressed but says that the Doctor must have begun fighting Daleks when he was very young.
The Doctor suggests that the station is being used for research purposes. Tranter agrees: it is a super-secret base in Earth-Space where prisoners are interrogated. He says that they use it to hold Robomen, Ogrons and things that were left behind (including Mechanoids) when Daleks ravaged other worlds. They even have a crashed Dalek scout ship among the Dalek technology that has been picked up but none of it works without the Daleks operating it. The prize of their collection is a room full of captured Daleks, ten in total, which have had their weapons removed and can run only on static electricity supplied through the floor. Tranter reflects on the irony of his situation: two months earlier he was a prisoner of the Daleks, now he is their jailer. His incarceration seems to be the reason why he has an artificial eyepiece to augment his vision. He tells them that the Daleks have inhibitors fitted so that they cannot store power and that the section of the ship they inhibit can be jettisoned and allowed to crash onto the planet Strantana below.
Tranter thinks that the inspection has been triggered because of Weston. He was the chief scientist on Station 7 for years and had recently claimed that he had found a way to make the Daleks less deadly and aggressive. Tranter's first objective when he took over the station was to stop Weston: the commander doesn't think that Daleks can be changed and opines that the only good Dalek is a dead Dalek. When the Doctor asks if he can see Weston's laboratory Tranter laughs at him but sends the young officer, Jay, to accompany the Doctor and Amy while they go to have a look. Jay tells them that Weston's work was progressing and Hadleigh, his deputy, seemed to be on the verge of a breakthrough.
When they arrive at Weston's laboratory they are shocked to find that the door opens onto outer space, albeit with a force shield. It seems that the lab was detached from the station by Weston just days before Tranter's arrival, probably by the scientist himself. The Doctor says that when Station 7 was used as an ore station this was how the freight pods would have been sent back to the planet. As they stare out into space, Amy spots something moving. Jay calls it in but the command centre replies that it is only a group of asteroids moving through the system.
Jay and Tranter accompany the Doctor and Amy to a presentation being made by Kustler (the new chief tech since Hadleigh died). He tells them that Hadleigh had switched the direction of research from Weston's genetic experiments to a digital approach. Kustler reveals a Dalek which he claims to have total control over. A positronic brain between the Dalek creature and the control linkages allows him to operate the casing without intervention from the Dalek itself. This causes a stir among the other scientists in the room but the Doctor and Tranter demand that the experiments be halted. Kustler argues that control over these Dalek casings will allow the humans to operate the other Dalek technology by proxy. Tranter says he will think about it but says that Jay must return the Dalek to the lock-up.
The Doctor and Amy walk with Jay and the Dalek. The guard tells them that this is only one of two that have been signed out. Hadleigh took the other with him to the petrified jungle. they see that the scientist had fed static electricity into the floor to allow the Dalek to move freely. The Doctor demands that this be shut off while he goes into the jungle. Amy wants to go with him but he gives her the task of keeping her eye on the asteroids while he and Jay lead three guards into the Skaro sector. The Doctor refuses a protective suit because it would slow him down.
Things go wrong across the station very quickly: one of the guards is attacked by a Varga in the jungle and his suit is ripped; the Robomen attack their guard after a mysterious signal bypasses the jammers; the asteroids change course to head for the station; they are scanned to show that they are 78% Dalekanium. Defence fighters are launched.
The Doctor and Jay, with their escort guards , find an orange Dalek. Despite the static being cut, the Dalek is standing by a metal lizard, a Magneton, from which it is drawing power. The guard who was attacked earlier, now transformed into a Varga, appears on the scene and causes a distraction for the Dalek to pick up the Magneton and crash it down on another guard's head. The Doctor asks the Dalek what it is doing there and it replies that it is waiting to be rescued. The Doctor and Jay, now the only survivors, flee to the exit where Amy is waiting to tell them that the asteroids have revealed themselves as Dalek ships.
Amy asks Jay how the Daleks can know about Station 7 but Jay is at a loss to know. The Doctor says that the important question is what the Daleks want. Kustler says that the Station has no chance of survival unless he is allowed to arm the captive Daleks and use their weapons against the attackers. Tranter refuses and Kustler accuses him of being closed minded. He says that is why Weston left after the 'last time'. When the Doctor asks what that means Kustler tells him that Station 7 was converted from an ore station years earlier and Tranter was sent there as a junior officer. When he heard Weston's plans he made his objections public but was redeployed due to Weston's seniority. Since then Tranter fought on the front line and earned both promotion and a reputation. Even though he was captured at the siege of Logario he escaped from the Dalek prison ship with several other people and escaped back into Earth space. When he was invalided out of the front line he took the job on Station 7 mainly, believes Kustler, to close down Weston's research. Tranter denies this and even agrees to let Kustler have his way. Now it is the Doctor's turn to object but Tranter says that the Daleks can only be attacking the station because they know the research is dangerous to them.
Kustler and his team remove the Daleks from the lock-ups and begin to convert them. They are numbered so that jay can tell which is which. She, too, has misgivings, as do the technicians working on the Daleks. The Dalek power pulses, like a giant heart beat, resonate through the station. It is a sign that the Dalek ships have broken out of their camouflage and are closing in on the station. A dogfight with the defending station fighters ensues while Jay places five converted Daleks at a point where the entrances are covered. Outside, the last of the fighters is destroyed. A Dalek saucer docks with the station and ranks of Daleks begin to move down the docking tubes. Kustler is forced to abandon his conversion process and leave the unconverted Daleks in the laboratory.
The Daleks begin to cut their way through the bulkheads. They send a signal to the Robomen and Ogrons to kill all humans and these prisoners burst from captivity and fight their way through the corridors. Jay orders the defenders to let them pass so that they can be killed by the converted Daleks. When the Daleks duly respond to Tranter's command, and slaughter the first prisoners to arrive, it seems that the plan is working. However, the Dalek attack force is now aboard the station and a second saucer is docking. The attackers take a number of casualties as they are ambushed but seem to think they are within acceptable parameters.
The Doctor wants Amy to get into the TARDIS while he tries to find out what the Daleks have come for. He says that he can save everyone if he can use the TARDIS. Amy objects but Tranter orders Jay to go to the petrified jungle with Amy to secure the Doctor's equipment. The Doctor says he wants to use the static feed to the floor, coupled with the station's engines, to send a massive energy pulse through the station. This will destroy Station 7 and the Dalek ships attached to it. They need to make sure all the humans are off the station by then so the Doctor says they should fall back to the lock-ups beside the jungle.
The Daleks continue to fight their way through the corridors, killing every human they meet and recovering or destroying Dalek equipment that they find on the way. They cannot find what they are looking for, though they name it as 'the abomination'.
Jay and Amy reach the TARDIS but it is being guarded by the unarmed Dalek in the jungle. They retreat, cautiously.
The Dalek attack force reaches the last line of defence - the converted Daleks. Tranter presses the switch that will cause the Daleks to open fire but nothing happens. Instead, the converted Daleks turn on the humans. The Doctor realises the conversion was all a trick. He orders the humans to retreat to the lock-ups. Kustler is aghast at what he has done but at least he knows why Hadleigh was killed - he discovered the Dalek deception. Sadly, this is the last thing he hears before he is killed.
Tranter and the Doctor lead a small party of security officers down the corridors. The Doctor accesses a terminal to blow the docking clamps in order to release the jungle section of the station. Daleks burst through the sealed doors and a gunfight rages around him as he does so. A stray Dalek shot breaks the window on the corridor, sucking a Dalek and a human out before the Doctor reconnects the force shield. The portion of the station containing the Doctor and Tranter, along with a handful of survivors, falls towards the planet. He thinks that Amy is on board that section too because it contains the jungle. As he gazes across at the station he sees Amy and Jay, still aboard.
Amy and Jay work their way through the station. They come across a damaged blue Dalek and realise that it was one of the converted Daleks. Not realising that the 'conversion' was a deception they leave it alone and try to move down a corridor but are caught by a party of Daleks searching for the abomination.
The Doctor tells the people with him that the capsule is sturdy enough to survive entry into the thin atmosphere of the planet. The capsules were designed to be dropped from orbit. Tranter realises that this is what Weston would have done.
All of the Ogrons and most of the humans on the station are dead. The Daleks withdraw control of the Robomen, leaving them to their fate. The Daleks surmise that the abomination must be on the jettisoned part of the station. They also identify the Doctor and order saucers to follow him down to the planet.
The section of the station crashes onto the icy wastes of the planet, breaking through the crust to reveal molten lava beneath. The survivors scramble from the vessel as it sinks but some don't make it out in time. The Doctor spots the TARDIS floating on the lava as he leads the remainder to safety. Their escape, meanwhile, is being observed on view screens from afar by somebody who recognises Tranter. No sooner have the humans got away from the lava than they are assaulted by a group of fierce creatures - tall, muscular and possessing sharp fangs. These creatures are driven off by a second group but the newcomers have been fitted with steam-driven servo-relays. Somebody has been messing with their brains. The second group seems much friendlier and leads the humans across the snowfields.
As a known associate of the Doctor, Amy is questioned about the Doctor's attempts to recover the abomination. Amy has no idea what they are talking about but does glean the fact that the Doctor is still alive. She is returned to a cell with Jay and tells her about her experiences. Jay shows her the control device for the converted Daleks and they begin to make plans for how to use it. Jay signals for a Dalek to come to their rescue. While she does this the saucer they are on moves away from the station and launches missiles. Station 7 is utterly destroyed. A red Dalek enters their cell. Amy and Jay rush it in an attempt to escape. The Dalek brushes them off and turns to exterminate them but the blue Dalek arrives in the nick of time and responds to the control device. It destroys the red Dalek and then leads them to escape via the scout ship the Daleks recovered from Station 7. As they leave the Dalek saucer, thinking that they have escaped, the Dalek command watches on. The women will lead them to the Doctor and to the abomination. To maintain the illusion a few missiles are launched at the scout ship and some flying Daleks block its path. These obstacles are overcome with some minor damage to the ship. It makes a successful, if rough, landing near to where the Doctor landed. The Dalek leads them across the snow, following the trail left by the humans that passed that way earlier.
Ahead of them, the Doctor and his party have been allowed through a hatch and find themselves in the old ore refinery. The Doctor recognises that they are being permitted to pass through the levels by a guiding hand (who is watching on remote cameras) and tells whoever is waiting for them that they will be there soon. As they traverse the underground base they see that it is using ice and lava to create vast amounts of steam power. This is an undetectable power source. They see a reactor, unused but ready for action. Several miles later they finally encounter their host; Professor Weston. He tells them that he was badly injured by the native creatures after he crashed but used steam technology to repair himself as well as to augment some of the creatures. He tells one of the creatures to provide food and drink for the visitors. While this is happening Weston tells the Doctor that the Daleks are approaching but they will not be able to detect his base.
Dalek saucers land near to the scout ship and ranks of Daleks disembark. Their first action is to rescue the Slyther that escaped from the crashed section of the station. Then they detect a signal from their agent in the foothills of the mountains.
Weston spots Amy, Jay and the blue Dalek on his screens. He prepares to send his creatures out to attack them until the Doctor tells him that Kustler tried to convert the Daleks and the two girls obviously think that the one with them is under their control. They decide to allow them to enter the base and then capture the Dalek so that Weston can use the casing. This brings the Doctor to ask about the Dalek creature that Weston is keeping in a jar. Weston plunges his hand into the jar to tickle the creature while pointing out how its aggressive tendencies have been removed. He has created, in essence, a good Dalek. Tranter reacts angrily to this, reiterating that the only good Dalek is a dead Dalek. He adds that the creature is an abomination.
Amy, jay and the Dalek find themselves following the route through the base that the Doctor took earlier. Their pursuers soon approach the outer doors. Weston prepares to send his creatures out to fight them but Tranter's last few soldiers say that they will go too. Protecting Weston's work is of paramount importance. Despite digging in before the Daleks arrive the defenders are quickly killed with few Dalek casualties.
Inside the base, Amy and Jay arrive at the room where Weston, Tranter and the Doctor are waiting. The 'converted' Dalek tries to kill the abomination but the Doctor jams a steam pipe into its damaged casing. This knocks out the Dalek creature long enough for them to remove it from its casing. Somehow the Daleks on the command saucer are able to watch this exchange and know where the abomination is. The saucer launches missiles to blow the doors of the base open. Weston cuts off the flow of steam from the generator so that the corridors ice up. This slows the Daleks' progress. The only thing to do now is to get out of the escape route and use the tamed Dalek creature to fly the scout ship away from the planet.
The Dalek creature lashes out with its tentacles but the Doctor and Tranter manage to manhandle it into a tank similar to the abomination's. So violent are the Dalek's actions that it cracks the tank but not enough to break out. Weston picks up a disc containing all of his research notes and findings. The Doctor uses the control panel in the room to set the nuclear reactor to critical in twenty five minutes. The only problem is that the safety measures will have to be disengaged on the reactor itself. While they are busy, Tranter takes the docile Dalek creature and puts it into the captured casing.
The Daleks are slowed by the ice-filled corridors and so release the Slyther to try to stop the escapees. It catches up with them at an intersection near to the reactor. Weston orders his Dalek to kill the Slyther but it protests that it has been taught to value life. The Doctor tells it to fire at the roof. It does so, causing the roof to collapse. Unfortunately, the rock fall breaks through the floor of the corridor and the Slyther tumbles into the molten lava. This also blocks the way for the escapees and they have to find another way to the generator room. This will necessitate opening bulkheads; Jay says she will go back to the laboratory to do this. For some reason Tranter follows her and the Doctor, suspicious, follows him in turn.
Jay opens the bulkheads but as she prepares to leave the laboratory she notices he two jars where the Dalek creatures were stored: the cracked one is empty, meaning that the tamed Dalek is still in its jar. Tranter enters and attacks her but the Doctor stuns him with a burst of sonic energy directed at Tranter's artificial eye. He says that Tranter is not in control of himself. He suspects that Tranter's time as a prisoner of the Daleks led to several things: interrogations revealed what Tranter knew of Weston's genetic experiments on the Daleks; false memories were implanted so that he thought he had escaped of his own accord; a desire to run station 7 was planted in head, too; a tracking device, camera and transmitter were placed in his eyepiece so that the Daleks could find the station. Tranter says that now he knows the Daleks are there in his mind he can feel them. The Doctor removes the eyepiece and crushes it underfoot.
The Doctor looks at the tanks and realises that Amy and Weston are with a real Dalek. There are only seven minutes left on the countdown clock and the Daleks are making progress through the tunnels.
The blue Dalek leads Weston and Amy towards a trap. Tranter runs off to the reactor to over-ride the safety devices. The Doctor and Jay arrive on the scene as the Daleks close in on Weston. He passes his data disc to Amy and pushes her through a doorway towards where the Doctor is hiding. The Daleks exterminate Weston while the Doctor breaks a steam pipe and brings an ice-fall down, destroying or blocking out the Daleks. Only the blue Dalek breaks out it sets out back to the laboratory to halt the countdown. It arrives with a red Dalek in time to stop the clock with three seconds to spare.
Tranter finds the reactor room already occupied by the Daleks. He pretends that he is still one of their agents. The ruse buys him the time to press the over-ride button and damage it so that it cannot be re-set but the Daleks tell him that the countdown has been halted.
The two Daleks in the laboratory pick up the jar containing the abomination, intending to take it for analysis and extermination. It starts to thrash about and cracks the jar open, then it pulls the lever re-starting the countdown. It utters the word, "Exterminate!" The reactor becomes critical and lava explodes out into the reactor room, killing the Daleks within and Tranter (who seems to welcome his fate). The lava flows through the corridors, wiping out the Daleks but not the Doctor, Amy and Jay who manage to climb up ladders to the emergency hatch. They emerge onto the surface to find that it has stopped snowing.
In the laboratory, the red Dalek blames the blue for failing to protect the facility and exterminates it. Before it can do the same to the abomination the lava flows in and destroys it. The abomination watches from the relative safety of a place on a control panel. The lava pours out down the mountain, sweeping away Daleks and causing the ice to melt under their saucers. As the space craft sink into the molten lava and explode only the bridge section of one escapes but is caught in the massive explosion of the saucer beneath it.
With all the Daleks dead, the Doctor leads Jay to the Dalek scout ship. He makes it ready for flight, even without a Dalek. Amy and Jay hug while Jay asks if the deaths of everyone on Station 7 were worth it to protect Weston's work. The Doctor says that the cost was terrible but the result was worth everything. Back in the TARDIS, which they find lying in the snow, he reassures Amy that Jay will be alright but Weston's data will have little practical effect on the outcome of the war.
Flying back to Earth, Jay contacts a young communications officer and says that she feels like a sitting duck in a Dalek ship. The officer reassures her that she will create a safe path for her as she knows what it is like to be a prisoner of the Daleks. When her superior officer asks who she was talking to, the communications officer says it was merely routine. As she turns to speak her left eye is revealed to be an implant exactly like Tranter's. Jay's ship crosses an asteroid field where a Dalek saucer is waiting for her.
The TARDIS passes through a huge space battle between Earth and Dalek forces. Amy asks how, if Weston's work is worthless, it was worth the death toll. The Doctor replies that it gives the humans the one thing that the Daleks can never destroy; hope.