Chicago, 2006. The Doctor has lost the TARDIS in a bet. Ian is fixing up a purple Oldsmobile 88 which the Doctor won in another bet. The Doctor and his companions are going to travel down 2500 miles of Route 66 to get the TARDIS back. The early part of the journey is fractious. Neither the Doctor nor Susan can drive and the Time Lord is particularly uncomplimentary about their vehicle. He is not enamoured by their stops for the likes of frozen custard. By Missouri some of his edginess is disappearing and by Kansas he is taking a turn at the wheel. Ian and Susan are positively enjoying themselves with only Susan worried that they won't get their TARDIS back and lose their way of life. By the time they are poolside in Texas all four are relaxed enough for Ian to jump into the water fully clothed. By New Mexico Ian and Barbara can imagine a future where they do not return to their own time but travel with the Doctor for as long as it takes and enjoy it. In Arizona, watching the Doctor explain the effects of an ancient volcano to some young children, Barbara recognises that the four of them are a family. At the end of Route 66 in California the Doctor checks into a hotel and demands internet access. Ian discovers him later that night on an auction site showing the TARDIS still in Chicago. The Doctor admits that the whole trip was a ruse to help them all to relax before he books aeroplane tickets back to Chicago.

Victoria wakes up dreaming of her father. Meanwhile, in a graveyard, an aged automaton waits. While Victoria is telling the Doctor that she needs to go out of the TARDIS for some fresh air the automaton sees three children. Despite its age and deterioration it can still close off their escape route. London is still recovering from the after effects of the recent Yeti attack. Victoria crosses London, remembering how it was in her day. She regrets not telling the Doctor where she was going. She arrives at the neglected cemetery and squeezes through the railings. She discovers the half buried remains of a child. The automaton recognises her and moves towards her, calling her name. It is supposed to resemble her father, but the face has peeled, one eye socket has been destroyed, circuitry is exposed and its limbs are damaged. Victoria runs away in horror but is cornered by the wall. The Doctor rescues her, thrusting his sonic screwdriver into the damaged eye socket until the machine is dead. The Doctor tells Victoria that it was placed by the Daleks near her father's headstone to wait for her. A century's wear and tear ruined it before she arrived. She looks at the Doctor and realises that even though she loves him he will never replace her father. Later, back in the TARDIS, she recalls seeing two names, her mother's and her father's, on the headstone. Two names when really there should have been three.

The Thrematons arrived on the Sabbath above the settlement, dropping dark fluid onto the houses from their ships. These ships then buried themselves in the ground leaving only the tips exposed. Two days later Roshon fell ill, vomiting. Spyrocysts erupted from his body. He and others left the settlement and went to the buried ships. Ptela went after his brother Roshon to rescue him from the Thrematon ship. Roshon's left side is a seething purple mass. Forcing open the bulkhead they rescue Jo from a Thrematon horde. Roshon sacrifices himself to let the other two escape. Jo and Ptela hide in the forest. Ptela has fallen in love with Jo. She tells him that she thinks the Doctor is dead, a dark mass exploding through his pores like jam through a muslin bag. She recounts the times that the Master used her to get to the Doctor and kill her. Ptela wonders why anyone would go to such lengths. The pair of them make their way through the newly frozen forests towards the invaders' ships. They scale the side of one, while the Thrematons spit at them from below. Once inside they are captured. Jo asks Ptela to hold her for comfort, which puzzles him at first. She tries to give him her locket, then remembers she lost it on her previous trip and gives him her ring. Ptela thinks this is a proposal and accepts just as the Doctor breaks in through the bulkhead. He tells Jo that the Thrematon's' attempt at genetic engineering would not work on his Time Lord physiology. He has also turned the heat up in the ship, killing some of the invaders. He tells their leaders to leave the planet. When they refuse he blows up their ships.

The Doctor and Jo take the injured Ptela into the TARDIS. An explosion has destroyed the invasion. The Doctor fetches a medical kit. Ptela considers ripping components from the TARDIS console to stop Jo from leaving. Instead he tells her that he is part of the Thrematon horde and lumbers out of the TARDIS. He heads back to the forest hoping that Jo will follow him but she calls for the Doctor instead. He leaves an obvious trail of broken foliage for them to follow. He arrives at the Thrematon masts, the remains of their devices intended to change the world to their liking. The Doctor said that they should be left as monuments to the downfall of the invaders. Tremors and explosions rock the landscape. Ptela changes course back to the settlement which now perches on the edge of a volcanic crater where the mother ship once stood. The Doctor reaches him there. Thinking that Ptela is under the control of the Thrematons he tries to hypnotise him, but Ptela pushes him into the crater. They tumble down the sides and the Doctor is submerged beneath the lava. Ptela gives up on his pretence of being under Thrematon control. He tells Jo that he loves her. The doctor reappears, showing off a Thrematon portable atmosphere device. Later Jo tells Ptela she is leaving. He asks her to stay or take him with her but she tells him the Doctor would not allow it. After she has gone Ptela remembers Jo's kiss, back in the forest, and thinks it is like a Thrematon device, planting something in his heart that changed him forever.

Tom Charrington, 18, and Emily Rutherford, 17, are in love but have to separate because of the discrepancy between their IQs. His is 137 and hers is 192. The government of the Earth Empire has decreed that couples with more than a fifty point gap cannot be given work permits or social service benefits, nor their children attend school. They are thus transported by Separation Day Inc. to an exact holographic representation of the library where they first met in order to make their parting easier. However, the library begins to darken and disintegrate around them. The TARDIS arrives and the Doctor and Sarah emerge. The Doctor tells Emily that he has received telepathic messages from a hermit on his home world informing him that this separation will set in train a series of events that accumulate to destroy the entire universe. The destruction around them is reality warning them of the ultimate consequences of their actions. The director of Separation day Inc. transports in to stop the Doctor but becomes hideously deformed and mentally distressed. The Doctor tells him to let go and the director explodes. Tom and Emily decide not to part and normality is restored to the library (and the universe) The Doctor explains that Separation Day was probably a front for a government research organisation trying to create and research into emotional strife. The director was a research organism that had become horrified by its own actions. The Doctor reminisces about his own feelings when Jo left him, not noticing the pain this causes Sarah. Afterwards the unpopular government is overturned by a more liberal regime and a better world ensues.

An opportunistic entrepreneur, Gruvengler, and his grew of G'Ug are abducting humans from Earth and using them as mercenaries for interstellar combat. They keep their abductees sedated by putting them into facsimile movie theatres to watch classic films while eating drugged popcorn. Android cinema attendants oversee the theatre but cannot prevent an infestation of giant space weevils from eating some of the humans. The Doctor and Leela, on their way to the steaming jungles of Kentillion 12, dematerialise near the theatre. Leela befriends Connie, a middle aged woman who, due to her aversion to popcorn, is well aware of what is going on. The Doctor confronts Gruvengler who explains that voyeuristic races in the galaxy are paying top dollar to see his army destroyed in a bloodbath. As Gruvengler tries to turn his zombified humans against the Doctor he realises that the Time Lord has used his sonic screwdriver to change their programming. They turn instead on the weevils which flee into the G'Ug control room. The G'Ug are thus persuaded to return the humans to Earth and the Doctor departs. Gruvengler is eaten by one last weevil.

The Doctor dreams he is in a rose garden surrounded by Autumn Damasks which he bought in eleventh century Persia when he was with Ian, Barbara and Susan. The garden and the roses are not real, merely a dreamscape he has constructed over the centuries as a place to retreat to. While in the garden he is surprised to encounter his first incarnation who is irritated by additions that were made to it by the second and third incarnations. The fourth Doctor is considering retiring to the garden and wonders if it is time to retire. He suggests that the first Doctor might be there as his guide but is met only with a sarcastic retort.

The TARDIS arrives in Maine. Romana is accompanying the Doctor as he attends the funeral of Hannah Gites. She was a poet who advised him on the cultivation of roses. Her daughter, who was clearly expecting someone else, gives him a book he left behind. Later, in the TARDIS, Romana sees him reading the book. Afterwards she finds it marked at Christine Rosetti's poem 'Remember' (Remember me when I am gone away/Gone far away into the silent land).

Back in the garden he is told by the first Doctor that the second planted forget-me-nots when his companions' memories were wiped. The third Doctor wanted to put in a statue but was refused. At the window of the Victorian house which stands in the garden the Fourth Doctor sees a blank faced white figure watching him and thinks of his successor. Afterwards he talks to Romana, wondering how he will be remembered when his next regeneration occurs. She convinces him that he has done enough to be remembered well and he seems to cheer up, offering to take her to Brighton.

The Necropolitan is an official place of mourning run by The Solemn Ones, omni-denominational and intra-dimensional funeral officials who cater for all races, religions and philosophies. As Verin, one of the senior attendants goes about his duties (including dealing with the officious Styles, shop steward of the mourners, and his own counterpart Cora) he encounters the Doctor and his companions on a number of occasions. Verin recognises him from previous visits and incarnations. At first the Doctor is a mourner but later, after the discovery of a corpse, he is helping the Solemn Ones track the killer. Verin sees him waking a revenant Solemn One (very much against protocol) and later rescues him from a locked cupboard. Finally he sees the Doctor being thanked by the solemn Ones and leaving with Nyssa and Tegan. Verin seems neither interested or concerned by the Doctor's actions, nor does he have a clear picture of what actually happened.

Tegan and Turlough are with the Doctor to witness the burial of the Master. Afterwards they head down to the nursing home where he died. They find a few of his possessions in his room. While Tegan goes to fetch tea the Master's coffin - his TARDIS - materialises in the hall. Laura, one of the nursing home's attendants, has discovered the doll-like remains of an old lady. Other patients have complained of strange noises in the boiler room. Tegan helps Laura investigate. In the furnace they find a number of burning miniaturised bodies before they are both confronted by the Master, or rather the burnt corpse he is controlling. Meanwhile the Doctor learns that the master was hideously burnt in his final days and only spoke to Mr Tase, the head of the home. While the Doctor looks for Tase Turlough is searching for Tegan. He finds her in a drawer in the morgue, still alive. She tells him about the corpse having the Master's TCE. The Doctor finds the Master in Tase's office. Tegan and Turlough are brought in by a group of patients under the Master's control. Turlough explains that none of the nursing home is real as the entire building dematerialises. It arrives in a forest. The Master is carrying a box with Turlough's miniaturised body inside it. He leads the Doctor and Tegan to a castle. Inside he explains that the Time Lords took away his last incarnation but his loyal TARDIS had brought his disembodied form a selection of humans, most of whom he killed. Eventually he ensnared the Doctor who claims he would help the Master if he knew how. Instead the Master ties the Doctor to a device intended to steal one of his incarnations. It fails, however, just as the Doctor felt the Master knew it would, Turlough is restored and the Doctor is left wondering what to do with the unconscious body of his enemy.

The Doctor and Tegan are taking the giant woodlouse Gravis from Frontios to Kolkoron. The planet they arrive on is muddy and forested, unlike the barren world the Doctor is expecting. The trio are soon attacked by a group of rather stupid armadillo type creatures, one of whom has a gift for prescience and a very pessimistic attitude. He tells them that his people are being pursued by mysterious enemies that destroy every planet they arrive on. The other armadillo's show great faith in Phoon's plan to let them save this planet, Queth, but they can barely agree on whether Phoon is even alive, let alone his plan. They all agree that this planet, Queth, is about to be destroyed. They eventually take the Doctor to an Echosphere in which Chaugh claims to have seen the future and as it was foretold he kills himself by leaping into an acid bath. His mental energy creates a five-pointed image map of localised phase-space. The Doctor realises that the more intelligent armadillos knew this would happen and sacrificed themselves for the salvation of their race. The Doctor cannot locate any enemies or cataclysmic events about to happen but knows that the entire planet is about to cease to exist. Gravis thinks he has saved the day when he shoots the image map with a gun that sends its targets to a pocket dimension. The resulting earthquake allows them to reach the TARDIS and escape. The Doctor drops Gravis off on Kolkoron as planned then travels back to Queth and back 300 years to let the 400 surviving Queeth evolve into their more intelligent descendants who will carry the memory of every planet being destroyed that they have inhabited, creating an endless unbreakable cycle.

The Doctor takes Peri to a cricket match and then treats her to some clothes shopping in London. He shows her to her room in the TARDIS and makes dinner with food from the vegetable garden. She is perplexed and worried by the vastness and complexity of the TARDIS's interior. More than that she questions the Doctor on his role in the various conflicts he has helped to resolve, wondering how he knows which side he should be on. He agrees that he often uses his instinct in these matters. Later he calls up program five on the TARDIS computer: a virtual representation of two species depicted in black and white pixels. He puzzles over how to help each of them reach evolutionary stability without harming either. The problem is beyond him and he is worried that the program is using up too much of the TARDIS's memory. Peri discovers him later that night, no clearer on how to proceed. He tells her he wants to solve the problem and deposit at the Proofrock-Mills Intelligence Museum, established in San Diego in 3009. After Peri has gone back to bed he sets the controls for the museum in 3010. When he finds the program in its exhibited state he does not recognise it at first: a swirling grey mass. He cannot fathom how this has been achieved. The most recent entry in the visitors' book is signed by The Doctor telling him 'You won't find the solution for a while. Give it a regeneration or two.' The next morning Peri asks if he solved the problem and he answers evasively, saying it wasn't so difficult. Then he tells her he has set the co-ordinates for a rain forest for them to explore.

A letter written by 36 year old Agatha Ellis. It describes her birth in 1970 which caused the death of her mother and the consequent mental illness of her father. She was bullied at school and was friendless from the age of ten. Her father died when she was 17. At the age of 21 she moved to London, hoping for a new start but settled instead into a repetitive, lonely life of routine. A chance encounter with a man called Godfrey gave her one night of passion and then he deserted her. She found she was pregnant. Four months into the pregnancy she finds Godfrey in her room again, his eyes glowing brightly, as is the baby within her. Her subsequent attempts to destroy the baby see her committed to a mental institution. She lies awake at night waiting for Godfrey to return. Instead the Doctor comes to her. He slowly builds her trust over a series of visits, giving her a few drops of medicine each time. One night Godfrey comes for her but the Doctor fights him and wins. He promises to return the next night and take her with him. Unfortunately he was so shaken by the fight that he left the bottle of medicine behind. Realising that the Doctor will never help her to escape herself she drinks the remainder of the bottle, a fatal overdose.

Morgan Sturgess is the founder of the Genetic Nuclei Exploration Corporation. An old man now he is about to hand over the results of his life's work to the government. Two hours before the government representative is due to arrive he finds the Doctor in his office. Fearing that the doctor is a terrorist like those who killed his rivals Sturgess calls for help but none is forthcoming. Instead the Doctor tells him he merely wants to talk. He tries to persuade Sturgess to destroy his work. Sturgess argues that it will benefit mankind, creating a stronger race which will live forever. The doctor does not explicitly say what will become of humanity but describes them as having 'a fixed face with a fixed tear in the eye for what was lost'. He shows him pictures of the future that will be brought about and then leaves. Sturgess blows himself up with the bomb the Doctor left behind, destroying everything in his office

Peter lives at home with his parents in Levenshulme in Manchester. His Dad, has just retired from teaching and is looking forward to a life of DIY home improvement. Peter and his Mum buy a set of wooden garden furniture from the Trafford Centre. The doctor is there, too, checking the furniture for unusual vibrations. He suggests they have a barbecue on Saturday and invite him. After the furniture is delivered Peter finds his dad sitting up at night on the wickerwork chairs in his pyjamas. He also notices a police box on the nearby Stockport Road which seems to be vibrating. The doctor emerges and questions him about the furniture before stalking off. Returning home he finds his Dad behaving in ways that are out of character and alluding harshly to Peter's lack of achievement. On the Saturday the barbecue is a raging success until the Doctor arrives and warns Peter about Goomba before striding off. Peter follows him to the TARDIS where the Doctor shows him a 3D movie of a giant tree with a face dating from pre-human history. This is Goomba and the garden furniture was made from him. By the time he returns home Peter finds the barbecue guests on the lawn building a giant effigy of Goomba which they begin to worship. Peter flees to the railway station but the Doctor tracks him down and takes him back to the TARDIS. He is in the process of dematerialising in the garden when Peter spills tea on the console. They emerge to find that several days have passed, the effigy is considerably larger (and on fire) and Peter's Dad is caged inside the head. The garden is full of worshippers. The Doctor keeps the alien spirit Goomba talking about its plans to use the worshippers as human sacrifices to power its escape to its own planet while Peter climbs up the back of the effigy and rescues his Dad. The old man falls unconscious on the lawn and Goomba's smoky spirit pours out of him. Later father and son are recovering in hospital while the Doctor takes Peter's mum for a trip in the TARDIS.

The Doctor wakes from a disturbing dream to find himself holding Steven's teddy bear Hi-fi. The TARDIS interior is freezing, probably to acclimatise its crew for what lies outside and the Doctor makes a note to uncover the code to stop this before it has fatal consequences. Leaving Ben and Polly in their beds he steps onto a mountainside at night with freezing winds howling. He recognises that he is home, in the place called Cadon or Lung. The lights of the Capitol shine below. As he climbs to the summit he wonders who has summoned him home. His mentor, sitting at the top of the mountain speculates that the Doctor brought himself home. It is the same night that he left his home world for the first time and he has returned via the same loophole. The two of them discuss, cryptically, the Doctor's purpose in the world and his ongoing fight against evil. Then his mentor gives back the Doctor's old diary which he kept as a young man. Thus he heads back down the slope with new heart to face whatever is in his future