Secret plans for a new weapon are stolen: components that form a part of that weapon are stolen; the thief is able to break through secure doors and electrified fences; guard dogs do not deter the thief; and guards have been killed. UNIT investigates and the Brigadier turns to the newly regenerated Doctor for help. The Doctor asks if all the components have been stolen and it transpires that one more component remains - a focusing crystal. The stronghold is fortified further and with UNIT troops patrolling the area nothing can get in or out. Yet something does, the thief strikes again - this time tunnelling under the stronghold and into the vault.

The Doctor surmises from the evidence that they are dealing with a robot. The question is who built the robot and why have they stolen the plans and components for the disintegrator gun? Sarah Jane Smith's own investigations take her to the Think Tank, an organisation comprising scientists. Among there number is or was a Professor Kettlewell who has built a robot. According to the director, Miss Winters, Kettlewell resigned. When Sarah breaks into Kettlewell's lab she encounters the robot. Later on, when the Doctor asks to see the robot he is informed that it has now been dismantled.

It is not long before it becomes clear that the robot is intact and that Miss Winters is part of an elite group, the Scientific Reform Society (SRS), which aims to create a better world. The robot and the gun will help them put their plans into operation. Near the Think Tank is a bunker and their the members of the SRS intend to hide out. The robot and gun have been used to attack another government official - this time to steal the launch codes for some of the world's nuclear weapons. It would appear the SRS intend to destroy the old world and rebuild it with their own chosen people...

Harry Sullivan's curiosity has sent the TARDIS thousands of years into the future. Emerging from the TARDIS, the Doctor warns Harry not to touch any more controls. As Sarah examines the walls of the dimly lit room they are in, the Doctor explains to Harry that they are probably on some kind of space station. Certainly the air is thin and beginning to dwindle as they breathe. Deciding that they will return to the TARDIS before the air runs out, the travellers continue to look around. Despite the Doctor's warning, Harry presses a button - this causes a door to open in one of the walls Sarah is investigating. She enters into the room beyond and the door closes behind her.

With the air supply thinning rapidly, the Doctor decices it is time to leave - but Sarah's absence causes him to ask Harry if he pressed any buttons. Seconds later they enter the room where Sarah is trapped. There, the air is even thinner, but the door closes before they can escape. Hurriedly, the Doctor seeks the atmosphere controls...and discovers the cables have been bitten through. Power restored, the Doctor places Sarah on a convenient couch and then returns to the TARDIS to get some medication for Sarah. Harry follows him...only to find that when the Doctor restored the power he also re-enabled an auto-defence system. While the Doctor and Harry hide from the defender and look for a way to deactivate it, Sarah vanishes and is transported to another part of the station. A voice informs her that he is now being put into cryogenic sleep.

Once the Doctor and Harry deactivate the auto-defence, they discover that Sarah is missing. An investigation of the couch reveals that it is part of a matter transmitter system and so the Doctor and Harry investigate the rest of the station in the hope of locating Sarah. What they find is a chamber containing all kinds of life, including specimens of the human race, all in cryogenic suspension. Sarah is not part of the system and unless they find a way to revive her she will remain a part of the collection until the station's own revivification system operates. The Doctor and Harry also discover the creature that bit through the cable system earlier...and a lurking menace on board the station that sees the sleeping humans as a food source for a new swarm...

Using the Nerva station transmat system, the Doctor, Sarah and Harry transport down to Earth. While the Doctor repairs the transmat system, Sarah and Harry explore the abandoned Earth, heading towards an area the Doctor claims to be Trafalgar Square. Instead, Harry falls down a pit which Sarah realises was covered. Unable to rescue Harry from the pit herself, Sarah returns to the transmat terminal to get help from the Doctor. However, the Doctor is missing, his sonic screwdriver abandoned. By now Sarah is aware that someone is stalking her and when she returns to the pit and finds Harry missing she begins to fear that some kind of mutation might live on Earth.

Although Earth has been abandoned, a small group from one of the colony worlds has been brought to Earth after intercepting a distress call. This group of men numbered 10 when they arrived, now there are five. The Doctor has been captured by three of the men - found standing over the body of a fourth. A fifth, Roth rescues Sarah from a robot patrolling the area near the pit. Roth does not wish to return to his friends - for some reason he distrusts them. Apparently it all has something to do with the creature that lives among the rocks...

Instead of returning direct to Nerva, the Doctor finds that he has arrived on some desolate planet. Another Time Lord emerges from the mist and informs the Doctor that they intercepted the transmat beam in order to send him on a mission. The Doctor refuses the mission until the Time Lord mentions one word: Daleks. The Time Lords have seen a future when the Daleks reign supreme - something must be done, at the time of their birth, either to destroy them utterly or hinder their development and perhaps make them less agressive. To that end, the Doctor and his two companions have been brought to Skaro, home planet of the Daleks. A war between the Kaleds and the Thals is continuing in the face of depleted supplies and recycled weapons, ordinance and clothing. Sophisticated technology sits alongside outdated devices or weapons.

The Doctor, Harry and Sarah wander across the surface of Skaro until they reach a trench just outside a vast domed city. An attack results in the travellers becoming separated: the Doctor and Harry are brought into the city; Sarah is knocked unconscious and left outside. The Doctor and Harry are treated to a speech about how the Kaleds will wipe out every last Thal and claim victory. It would also appear that a lot of advances in weaponry and the hopes of the Kaled people are placed in the hands of the Scientific elite, led by Davros. Escorted further into the city, the Doctor and Harry begin to learn more about the war and two factions. Most importantly, they learn that Davros is developing the Mark 3 travel machine for the mutation that the Kaled race will become ultimately as a result of the long war. Sarah, wandering around the outskirts of the city, witnesses a demonstration of the Mark 3 travel machine...something history will know as a Dalek...

The Time Ring given to the Doctor by the Time Lords returns the three travellers to Nerva...albeit in a different time zone from where it was left. As they need freedom to move about, in case the TARDIS arrives in a different section, the travellers explore this earlier version of Nerva. To their horror, the corridors are lined with corpses - all left to die it would appear. One end of the corridor is sealed, but the Doctor unlocks the door and they proceed through to the area beyond.

Warner is monitoring space traffic near Jupiter: a new moon has been captured by the gas giant and until every ship has a record of its position, Nerva must continue to act as a beacon, informing all passing ships of the new object. A crewman from a passing ship enquires after his brother. Warner, after checking with Commander Stevenson, informs the man that his brother is busy with the rest of the team. In reality, the man, like most of the crew is dead, killed by some mysterious virus. Consequently, the beacon is quarantined and only four remain - three crew and one civilian. A signal from the new moon, Voga, seems to suggest that there may be life down there. Kellman, the civilian and an exographer, refutes this stating that he has been down on Voga many times and its just a lifeless lump of rock.

When the Doctor opens the sealed door, it triggers an alarm - Stevenson and Lester run off to investigate. Warner is attacked by a strange metallic creature and while he lies dying, Kellman steals the log tape upon which was recorded the mysterious message from Voga. The Doctor, Harry and Sarah are accused of spreading the virus, but the Doctor quickly asserts that something else is happening. It is not long before the Doctor determines that the virus is really a poison and that Kellman is in league with the Cybermen. It would also appear that Kellman is working with the Vogans: one faction, led by Vorus intends to lure the Cybermen to Nerva in order to destroy them. Will his plan succeed or will the Cybermen destroy Voga, the planet of gold?