Towards the end of the 21st century, two major superpowers stand ready to destroy one another. Sea Base 4 is one of a number of underwater bases monitoring for possible enemy attack, ready to make the required counterstrike. Every so often a computer simulation is run to test the base personnel's readiness. A radar alert to something moving through the water warrants a further scan: but nothing is detected so it is assumed that is probably nothing more than volcanic debris; an unmanned reconnaisance probe is launched, just in case; and the base remains on alert. The probe is destroyed but the scanners still only show marine life! An orbital sentinel then engages a mysterious object which fails to respond appropriately. The object is fired upon, but disappears. The computer begins an attack run. Is it a simulation triggered by these events or is it a real attack? Maddox, a student on attachment, but the station's only sync operator, must plug into the base computer to either confirm the simulation or launch real missiles. The stress proves to be too much and he collapses.

An attempt to show Tegan her planet in the near future, the Doctor has overlooked a fault or two and the TARDIS had materialised in Earth orbit. The Sentinel Six Orbital Probe requests authorisation but when the TARDIS crew fail to do so, the probe fires upon the TARDIS. As it plunges towards the Earth, the Doctor manages to dematerialise the TARDIS and then rematerialise...inside Sea Base 4. Wandering around, the Doctor, Tegan and Turlough try to find someone they can explain their presence to. Unfortunately they end up being identified as intruders and saboteurs. While the crew of the Sea Base concentrate on stopping the Doctor and his friends, threats from both within and without begin to converge...

Most of the village of Little Hodcombe is taking part in a war game, celebrating the day in 1643 when the English Civil War came to the village. Local school teacher Jane Hampden is one of those not taking part: there are too many who get caught up in the ethos and take their roles a little too seriously. Despite Sir George's insistence that her involvement might temper such high spirits, Jane refuses his offer.

The Doctor is fulfilling his promise to take Tegan to meet her grandfather in the village of Little Hodcombe. At first, she believes he has broken another promise as the TARDIS has materialised in a crumbling crypt and immediately outside is a figure dressed in medieval clothing. The mystery figure eludes them leading the travellers into the derelict church above. Further uncertainty about where and when they have arrived is fueled by a group of soldiers on horseback coming across a field and encircling them. Brought to Sir George, the travellers receive an explanation. However, when Tegan explains they are there to see Andrew Verney, her grandfather, the tone changes. It appears he has gone missing and little effort has been made to find him.

Various phantoms appear now and again, some simply projections, others seeming more tangible, such as Will Chandler who bursts out of a priesthole. He entered the priesthole at the time of the original conflict, in 1643. On learning that Verney was studying the legends of the Malus, the Doctor begins to realise that perhaps its not a legend after all and the war games have a far more sinister purpose.

Fleeing the death of planet Earth, one group of humans have found their way to the Veruna system. A systems failure led to their ship crashing on the planet they have named Frontios. Since then they have tried to survive the frequent meteor storms that impact on the surface and the people who disappear under mysterious circumstances. There are tales of Frontios burying its own dead. When colony leader, Captain Revere vanishes, his son, Plantaganet takes charge. Assisted by Brazen, Plantagenet does what he can to keep the colony together, to combat the retrograde menace - those who wish to set themselves apart from the colony, and to discover the truth behind the bombardments. One thing is clear - it is some form of attack which they will not allow to destroy them.

The TARDIS has drifted far into the future, and is hovering at the edge of the Veruna system. The Laws of Time do not permit the Doctor to go any further: they can watch, but nothing more. The decision is taken out of his hands when some force pulls the TARDIS down towards the planet of Frontios. Caught up in the latest bombardment of the planet, the Doctor cannot ignore the plight of the injured he sees around him and renders some assistance. A lack of good lighting makes the task more difficult so the Doctor asks Tegan and Turlough to get portable generators from the TARDIS. They return, without the generators - the interior doors of the TARDIS appear to be jammed. Despite his offer of assistance though, the Doctor finds himself under suspicion. Have the people of Frontios finally come face to face with their enemy?

Stien and Galloway are among a group who break out of a warehouse. Policemen emerge and gun down all that they see. The police inspector activates a device and both him and the bodies vanish. The other two policemen resume their patrol as if nothing happened. Stien and Galloway emerge from hiding and return to the warehouse in the hope of finding the entrance to the time corridor. Unfortunately, Galloway finds something else and so Stien alone survives.

The psuedo-police inspector, Lytton, has returned to the Dalek ship, bemoaning the loss of valuable specimens. Now it is time to continue with their mission. An attack is launced against a space prison facility: the prison itself is in a state of poor maintenance and so its defences are easily smashed. Mercer orders that everyone must fend for themselves but sends two people to destroy the prisoner. They are caught and killed before they can succeed and now Lytton can reanimate the prisoner from hibernation - Davros, creator of the Daleks. The Daleks have returned for Davros because they are losing the war against the Movellans. They also promise to present him with another prisoner - the Doctor, who is walking into their trap.

The Doctor is waiting for the correct moment to escape from the time corridor in which the TARDIS has become trapped. Breaking free, he takes the ship to one end of the corridor - present day Earth. Finding Stien, the Doctor also encounters a small squad of soldiers at the warehouse. There under the guise of a bomb disposal squad, they are there to look into some strange objects which do not appear to be of Earth origin. A more immediate problem arise when a Dalek emerges from the time corridor...

Timanov tries to explain to Malkon, the Chosen One, the value of sending unbelievers to the fire. While some dissent is tolerated, sending the occasional free-thinker to the flames encourages faith. Malkon does not know if he has the strength to sacrifice anyone, but Timanov assures him that Logar will give him the strength. Timanov also remarks on the damage caused by the unbelievers and that every day they live in the shadow of the fire mountain. Without sufficient belief the fire will destroy them all. His authority is challenged by a group of unbelievers, especially after Amyand and Roskal return from the fire mountain: they saw nothing, and certainly there was no sign of the fire god, Logar. Just as it seems that the people's faith in Logar and Timanov is about to waver, the mountain rumbles. A lookout also informs the people that something has appeared in the ruins - could this be the messenger from Logar, come to save them from the fire?

Kamelion is plugged into the TARDIS computers and appears to suffer some kind of seizure. The Doctor checks on Kamelion and asks Turlough to check the console. Turlough is alarmed to discover that the signal is a Trion code and he tries to block it. The Doctor, however, is able to trace the signal to the island of Lanzarote, on Earth. They encounter Professor Howard Foster and his underwater team exploring nearby wrecks for relics. Foster's stepdaughter, Peri, trying to sneak off on an unauthorised gap-year trip to Europe, nearly drowns but is rescued by Turlough. He finds a Trion signalling device among her possessions. The Doctor returns to the TARDIS and determines to locate another signalling device: next stop the planet of Sarn. When Howard Foster appears in the console room to thank them for saving Peri, the Doctor is annoyed to have two new passengers. While the Doctor and Turlough explore the ruins outside, Howard, watched by Peri, transforms into the Master...

The twin worlds of Androzani Major and Androzani Minor could not be more different. Major is a heavily populated planet where people eat, work and sleep. Minor is a desert-like world with a molten-mud core and, when its orbit take it near Major, a tidal effect causes the core to blast out through blow-holes, the so-called Caves of Androzani. Yet, deep within those caves live a species of giant bats. These bats weave nests from a substance called spectrox. When refined, spectrox extends life - a boon to those who can afford it. The supply and distribution is maintained by a powerful business man, Morgus. The spectrox itself is mined by an android workforce - but Sharaz Jek controls the androids and the supply of spectrox. Betrayed by Morgus during a business deal, Jek has dug in deep into the Caves of Androzani, his androids programmed to kill any human who approaches. To that end, Morgus is supporting a military operation, led by General Chellak to locate Jek and arrest or kill him and regain control of the spectrox supply.

Chellak's operations also involve trying to stop the supply of weapons to Jek. Gun runners manage to slip through now and again, and with these smuggled weapons, Jek can keep up his defences. Given enough time, the people on Major will accede to Jek's demands: Morgus to be handed over to him. With time running out, it appears Chellak might have scored a victory, for his men have intercepted a weapons shipment and the gun runners. Naturally, the gun runners, called the Doctor and Peri, protest their innocence. However, sometimes the innocent suffer too - which does little to reassure the Doctor and Peri, especially when they are sentenced to execution before a firing squad. At least they won't have to worry about the itching caused after they both came into contact with a large, fuzzy sticky ball. Until they learn that they have contracted spectrox toxemia as a result of touching raw spectrox. In its raw form, spectrox kills within 48 hours and there is no known cure...

Before he leaves on business Professor Sylvest has a discussion with his twin sons, Romulus and Remus. Taught that respect must be earned, the twins express their contempt for their mother. They state that they want to play Equations, much to the concern of their father. He tries to explain that their mathematical skills could change the material world! Romulus and Remus dismiss his concerns as melodrama. After their father has left, the twins receive a visitor. Introducing himself as Professor Edgeworth he states he has come to pay respects to the twins' father. Taking note that he should not be there while the twins' parents are not present, Edgeworth bids farewell, shaking the boys' hands in turn. Under this guise, Edgeworth attaches drug discs to the boys' wrists. Then all three of them depart. Upon learning of this, the Earth authorities dispatch a squadron of ships to attempt to rescue the twins: their abilities cannot be allowed to fall into the hands of the wrong people. The squadron, however is destroyed, within the vicinity of the planet Titan 3.

The newly regenerated Doctor starts to become increasingly unstable, his moods swinging from delight to terror, from hope to despair. He even tries to attack Peri, believing her to be a threat. Horrified at what he has done, the Doctor concludes that he should go into retreat until the universe is safe from him. So he takes Peri to a barren world far from anywhere: Titan 3