Shortly before Benny’s time, several human colonies declared their indepdence from Earth, only to come back to the fold during the Dalek Wars. In the intervening time, the Seven Planets of the Althosian system were destroyed, and nobody has ever learned why. The Doctor has been in an odd mood recently, distant and distracted and paying little attention to his surroundings, and to snap him out of it Benny suggests that they investigate. The Doctor’s curiosity is piqued when he finds no mention of the Seven Planets in the TARDIS data banks, and he thus sets course for the Althosian system. However, the TARDIS encounters interference as if from another TARDIS when it attempts to materialise, and stalls in mid-flight. The Doctor seems to give up, telling Benny that sometimes they must just wait to see what happens next, and admits to her that his one fear is of the point at which there is no hope. He eventually thumps the console with his fist, and the TARDIS jolts back into flight and materialises on the system’s giant unnamed Planet. There, the Doctor determines that some external force is affecting his ship’s power systems, and sets off to investigate.

There are others on the Planet. The shapeshifting criminals Butler and Swarf have stolen the ultimate weapon, Pandora’s Box, which is capable of destroying the entire solar system if used, and are taking it to an ancient castle on the planet. They are accompanied by a team of enslaved khthons, the natives of the Althosian system; the khthons’ leader, Chopra, can read minds and perceive the future, but all he can see now is death and destruction. However, the shapeshifters refuse to heed his warnings that they are all pawns of cosmic forces beyond understanding, and that Armageddon is nigh. Meanwhile, the Archon of the Seven Planets concludes that Butler and Swarf must be terrorists, and, refusing to negotiate, he sends a team of Killer-type androids to recover the weapon and kill the shapeshifters. The androids land on the Planet, but are separated from their team leader, Spike, who is badly injured when his descent chute fails. The others realise that they will have to kill him when they next meet, in case he is one of the shapeshifters in disguise. They don’t know that if they fail to return, their ship has been programmed to self-destruct, and to destroy the entire solar system as it does so.

Meanwhile, the Seven Planets are descending into chaos. Fearing that Earth will retaliate for their declaration of independence, the government has allocated most of the system’s resources towards a massive and unnecessary military buildup. As a result, people are starving, essential services have been cut, and social order is breaking down. Major John Carlson of the Justice Police, unable to stem the tide of chaos, is trying to bury himself in his job, but the grim nature of his work is taking its toll on his health and his marriage. When a young girl with a promising future is found savagely murdered in a ritualistic manner, Carlson investigates but is unable to find any leads -- until a prostitute in the riot-torn inner city is killed in the same manner, and witnesses report seeing an antiques dealer, Bulbir Singh Mann, breaking into her flat and stealing a book of poetry by William Ashbless. Mann is arrested, and the khthon called in to read his mind determines that he is hiding something -- but that he did not commit the murders. Carlson is unable to hold Mann due to lack of evidence, and Mann is released at the direct request of Academician Brown, the leader of the government’s opposition. Carlson’s superior, General Kopyion, reveals that the “prostitute” was in fact an undercover Justice Police agent investigating an unrelated case. Meanwhile, riots continue to tear the city apart; despite official denials and propaganda, the government is in a state of collapse.

The Doctor and Benny find Spike, but when they try to tend to him he arrests them, believing that they are the shapeshifters. As they flee, the Doctor suddenly vanishes into thin air, and before Benny can do anything about it the other androids arrive, find Spike and Benny together and open fire upon them. Some external influence is affecting their weapons’ targeting systems, however, and Spike and Benny escape. Still believing that Benny is one of the shapeshifters, Spike demands that she take him to Pandora’s Box, and she has no choice but to accompany him onwards, to a nine-kilometre-wide river. There, Spike builds a raft, and to Benny’s surprise, he prays for success before launching into the river. There is a dim glow in the distance, and that is where he decides to head for, shooting everything that moves on the way in case it is a shapeshifter trying to sneak up on him.

The scientist Jarak and his wife Ell are also on the Planet, on a secret mission for Brown, but the very nature of the environment seems to be changing around them, which does not meet Jarak’s expectations. The river water turns red before his eyes, and when he tries to take a sample he burns his hand -- and freezes solid, dying before the horrified Ell’s eyes. She is unable to do anything as the redness creeps out of the river and paralyses the rest of the clearing, forcing her to retreat into her hopper. She cannot make sense of the data which Jarak has collected, or the conclusions he was drawing from it. This is not how things were supposed to happen…

The Doctor has fallen through a hole in Time into a hellish netherworld, where despair is an almost tangible force. There, the brutal, pig-like Cun set an angry marmoset on him and place bets on his survival. He survives the attack, and meets another accidental visitor to the netherworld -- poet William Blake, who fell through a hole in Time in Cambridge, and is convinced that he is in Hell. The Doctor and Blake find that nobody can be bothered to prevent them from escaping, and try to flee back to the hole in Time, but on the way, they are attacked by blue-skinned savages riding pterodactyls. The Doctor finds a child’s toy in his pocket and trades it to the savages for their freedom, but is concerned by the implications of their encounter -- for the savages spoke fluently in ancient Gallifreyan.

General Kopyion was one of the first Althosian settlers, and is a long-time associate of Brown, who has often played games of snakes and ladders with him. This is the chosen game of the elite on this world, where random chance is seen as the true guiding principle of the Universe. Kopyion escorts Brown to a meeting of the Academy, where the Archon tries to make a statement restoring order -- but Brown challenges the government’s authority and demands that social services be reinstated. The military representatives insist that martial law be declared and seem to be preparing for a coup, while the priests declare a holy war on the forces of evil, convinced that the chaos is a sign of the end of days. The government’s collapse can no longer be denied, and the Archon retreats to his palace -- but during the night he too is killed in the same ritualistic manner as the other two victims. Carlson’s wife Melanie, unable to deal with his growing depression, leaves him and volunteers her services as a nurse in the riot-torn sectors of the city, leaving him alone with his despair.

The Doctor and Blake find another hole in reality, but when they pass through it they end up in Whitechapel at the time of the Ripper murders. Blake is appalled by the casual brutality and degradation he witnesses, and realises that the social revolutions sweeping his era will not result in an Earthly paradise after all. The Doctor seems determined to solve the murders, but doesn’t know where to start, and when he enters a brothel to ask the prostitutes for help, he is taken aback when they mock him and demand money. Furious, and unable to understand why he is powerless against apathy in the face of evil, the Doctor admits to Blake that he’s beginning to question whether any good ever comes out of his interference. His sonic screwdriver is stolen by a street urchin, and when the Doctor tries to track him down, the urchin’s gang beats up him and Blake and delivers them to a Fellowship whose members worship the forces of evil to fill the void in their empty lives. The Fellowship attempts to sacrifice the Doctor and Blake, but the Doctor manages to escape from his bonds and burns the Fellowship’s meeting place down.

The androids are convinced that the shapeshifters are ahead of them, and thus they have not been watching their backs -- and Butler, having heard them firing at Benny and Spike, believes that they were offering him a challenge. He stalks the androids through the forest, playing cat and mouse with them and killing them one by one, until finally only the android Thomas remains. But Butler fails to appreciate the significance of the red weed they are approaching, until Thomas flings him into the midst of it and Butler dies like Jarak before him, frozen in Time. Even the birds are frozen in mid-flight over the contaminated area. Thomas, puzzled, follows the edge of the red weed until he finds Ell’s hopper -- where Ell triggers the ship’s self-destruct and flees, claiming that she found a bomb on her ship and barely escaped with her life. Thomas’ suspicions are lulled for the moment, and he agrees to protect her -- as long as she does not get in the way of his mission.

The Doctor and Blake find and pass through another hole in Time, only to be arrested by UNIT troops guarding an archaeological site on present-day Salisbury Plain. The Doctor provides his UNIT credentials to Colonel Philips, who shows him what the archaeologist Roberts has found -- the ancient fossil of a gigantic alien Monster. The Doctor, fearing that the creature is only dormant, demands that it be destroyed, but Phillips is taken aback by his attitude; the fossil is to be taken to the Natural History Museum for study, and UNIT will be escorting it. The Doctor realises that Roberts expected to find the bones here; in fact, Roberts is a member of the Fellowship, which survived its encounter with the Doctor in Victorian London. The Doctor and Blake accompany the escort to London, but they are interrupted when a group of Hunters -- demonic scavengers which cluster around holes in Time -- bring down a passing airliner and the escort is diverted to save the passengers. The soldiers are heavily outnumbered, however, and the Doctor, knowing that there is nothing he can do for them, steals the juggernaut with the fossil and drives it back to the hole in Time. Blake accompanies him back into the netherworld.

Benny and Spike land near the castle and continue on foot, and on the way Benny nearly falls into a quicksand pit. She is rescued by a mysterious figure whose face she cannot see, who tells her to remember the Empire that Never Ended. Further on, she and Spike find the ruins of an ancient, alien space station, but as they explore, Swarf learns of his brother’s death and sets off to avenge him. He finds and nearly kills Spike, but Benny manages to avoid him, and he eventually gives up searching and returns to the castle, dissatisfied. Meanwhile, Thomas and Ell are attacked by a snake, but when Thomas kills it he discovers that it is mechanical; this entire planet is a fake, apparently built by General Kopyion’s company Mirage Enterprises. He and Ell are attacked by a Hunter, but escape, and meet Benny in the ruins of the space station. She tells Thomas of Spike’s death, and accompanies him and Ell to the castle -- unaware that Spike, although grievously injured, is not in fact dead.

Brown returns to his apartment, knowing that the military is preparing to stage a coup and that even they will not be able to stem the tide of chaos. Humans are animals, doomed to the pit. Mann arrives with the book of “poetry”, which opens to reveal three bags of illegal drugs. He and Brown sample the drugs, and Brown has a vision of a Universe finally under his control -- but his rage and helplessness overwhelm him, and he is frozen in a tide of spreading red. He wakes with horror from his vision, just as an intruder shoots both him and Mann. Carlson intends to investigate, but Kopyion closes the case, telling him that the dead undercover agent was investigating Mann for drug smuggling and that Brown was Mann’s government contact. Carlson is dissatisfied with the explanation, but before he can investigate any further he learns that the government has turned chemical weapons on an “unruly mob” which had gathered to demand food -- and that his wife was killed in the attack. He tears apart the Justice Police file room, seeking an answer to the chaos engulfing his world, but finds nothing of use. Kopyion claims that these are the final days and sets off for the spaceport, to travel alone to the unnamed Planet. Seeking reason where there is none, Carlson concludes that Kopyion is responsible for the murders, in order to spread panic and anarchy and bring down the government so he can seize control when he returns with Pandora’s Box. He tries to kill Koypion, but Kopyion shoots and kills Carlson instead, with the same weapon he used to kill Brown and Mann.

As Benny, Thomas and Ell approach the castle, they encounter typewriter insects which print out useless and contradictory messages. Chopra senses the arrival of intruders, and Swarf sends the khthons to capture them. Ell, seeming to gain confidence as they approach the castle, insists that they surrender in order to get inside without wasting time, and as the khthons take them to the dungeon, Benny notices that the castle walls are decorated with the Seal of Rassilon. The khthons have taken apart Pandora’s Box and are using its power source to operate a dimensional drill, and as they switch on, Swarf eagerly anticipates the money he will make selling drugs from the netherworld. The red weed continues to spread towards the castle and Hunters mass in the sky as if waiting, but Swarf simply seals off the doors, insisting that he is in control. Chopra knows better; Swarf is a pawn, and soon the Monsters will be here. Meanwhile, Spike is captured by Hunters and taken to their nest, but their acidic saliva restores functioning to his lower limbs. He kills his captors and begins crawling towards the castle, determined to complete his mission.

The Doctor now knows the netherworld to be the domain of the Yssgaroth, the masters of evil who once ruled the Universe before the dawn of history, when the Time Lords drove them out after a long and bloody war. The Cun and the dog-like Galks are mining Dream B, a hallucinogenic drug from the netherworld which the Fellowship uses in its rituals, and are building a bridgehead by the hole in Time, paving the way for the Monsters to invade the Universe once more. The Doctor tries to stir up the Cun’s slaves against their masters, but they spit in his face and continue with their work. Desperate, he tries to use the explosive raw Dream B rocks to blow up the bridgehead, aware that this will kill him and only delay the Yssgaroth slightly, but unable to stand by and do nothing. Before he can detonate the explosives, an invisible force drags him and Blake back through the hole in Time and deposits them in a cell guarded by a computer defense system.

While waiting for their captor to arrive, the Doctor confesses to Blake that the legends of the Time Lords’ war with the Yssgaroth and their Vampire servants are just that -- legends. There are no factual records of the War in the history of Gallifrey; it is as if the Time Lords are trying to hide something. Their rescuer and captor is then revealed to be Kopyion -- or, as the Doctor knows him, Kopyion Liall a Mahajetsu, the legendary Time Lord general who led the war against the Vampires. He has been waiting for them to return for millions of years, but now he fears that he has made a grievous mistake by rescuing the Doctor and Blake. To the Doctor’s horror, Kopyion claims that the holes in Time were ripped open by the first experiments of the Time Lords; it was Rassilon himself who released the Monsters on the Universe, annihilating billions. The Time Lords eventually fought them back, but, knowing that the war was their fault, Rassilon erased the truth from history, refusing to accept Kopyion’s claim that what they had fought was pure Evil. Kopyion retreated to this system, built the Planet using Gallifreyan technology, and sat back to await the return of the Monsters. Now they are here, but he is unwilling to show his hand too early -- and if this means that Benny must die before he is ready to act, then so be it.

Ell, Thomas and Benny trick their khthon guards and break out of their cell, but Ell makes for the courtyard -- where she reveals that she and her husband were members of the Fellowship, as were Brown and Mann. As well as conducting ritualistic murders on Nicaea to celebrate the return of the Yssgaroth, they hired Swarf and Butler to steal Pandora’s Box and use its power source to drill through into the netherworld. While the shapechangers believed that their intention was to mine the deposits of Dream B that exist in the other world, their real intention was to widen the hole in Time so the Yssgaroth could swarm through. Thomas attempts to kill Swarf, but Swarf kills him instead, and Ell kills Chopra and waits for her masters to arrive. Kopyion’s enemy has been revealed at last, but as he prepares to confront her, Spike finally reaches the castle -- and with the last of his strength, he shoots the mining machinery, which explodes.

Ell is crushed to death when the castle collapses, but Kopyion beheads her anyway. Swarf tries to flee, only to be caught and eaten by a Hunter. The force of the explosion has been directed through the hole in Time, causing a holocaust in the netherworld and putting paid to the plans of the Yssgaroth -- for the moment. Kopyion knows that this was only a skirmish, to test his spirit, and by rescuing the Doctor and showing that he valued one life above the whole Universe, he feels that he has failed. To show his strength of will, and to prove that he will stand against the Yssgaroth whatever the cost, he decides to let the androids’ ship self-destruct and destroy the entire star system. Benny is horrified, but the Doctor reminds her that this is just what they came here to investigate; the destruction of the Seven Planets is part of history, and it cannot be averted. Kopyion decides to erase the truth from the Matrix, as it’s too dangerous to be known, and orders the Doctor to stay out of his way in future on pain of death. The Doctor and Benny, subdued, return to the TARDIS to take Blake back to his own time.