In the 1920s, Lucas Seyton, the gentleman thief known as the “Fallen Angel”, saves a man named the Doctor from androids which have pursued him to London. The Doctor explains that he and his friends recently arrived in an alien prison disguised as an English country home; Jamie and Zoe are still trapped inside the house, surrounded by android guards programmed to kill any intruders on sight. Seyton and his pilot friend Ketters help the Doctor to infiltrate the house, where they find that the alien prisoners are all dead, having turned on each other and slaughtered themselves. The android guards, which were not programmed with instructions in the event of their charges dying, keep trying to kill the intruders, but Seyton and the Doctor manage to dispose of them and rescue Jamie and Zoe. The Doctor arranges for the prison to be shut down by its absentee wardens, and as he departs, the prison’s mental safeguards erase all memory of the event from Seyton’s mind.

Time-Placement: The only real evidence for the placement of this story is the crew of Zoe and Jamie. This story may be seen as foreshadowing the meeting of the second Doctor and the Time Lords in The War Games, so I’ve placed it as a prologue to it.

Continuity Note: Lucas Seyton later makes a cameo appearance in the novel The Shadow of Weng-Chiang.

The Master assembles the fragments of the Godhead, an artefact of unimaginable power from the distant future of the Universe, and travels to 1930s Chicago, where he disguises himself as a mob boss while he tries to steal the last fragment from the Wainwright Museum. Before he can do so, however, his TARDIS is itself stolen. Grace Wainwright, the curator of the museum, turns out to be the guardian of the Thought Core, and she warns the Master that he is being used by the Godhead to assemble itself. It is the Thought Core which has possessed his TARDIS, and sent it to collect the remaining fragments; now it is on its way back, but without the Thought Core the rest of the Godhead is a fragmented creature with no control over its base instincts. Wainwright is killed by the Master’s secretary, who is herself under the control of the Thought Core. The Master, his hypnotic powers suppressed by the Core, flees with Wainwright’s silver bracelet, which is in fact a mercury fluid link which the Godhead requires to complete itself. He hides out in a homeless shelter, trying to remind himself of the discipline he learned at the Academy and regain control of his own mind. Eventually his TARDIS returns, bringing the Godhead with it, and when the Godhead tries to force him to bring it the bracelet he realises that it requires a living mind to complete itself. He refuses to submit to it, however, insisting that he remain in control. As the Godhead attacks him, he flees to the shelter’s kitchens -- and just as the roof comes down on him, the Doctor’s TARDIS materialises. The Fourth Doctor and Sarah are in need of mercury to repair their ship, and they emerge, find and take the fluid link and depart, unaware of the chaos breaking out just beyond the doors. While the Master lies trapped beneath rubble and the Doctor’s TARDIS, the priest who runs the shelter is accidentally exposed to the mercury which spilled out of the fluid link, and joins with the Godhead, providing it with the spiritual purity it requires to stabilise itself. The Godhead returns the Master’s TARDIS and departs to explore the Universe, as does the Master, thwarted once more.

Time-Placement: The fourth Doctor has Sarah exclusively as his companion placing it between Terror of the Zygons and The Hand of Fear.

Continuity Note: The Ministers of Grace originate from near the end of the Universe, a time the Doctor visits in The Infinity Doctors, Timewyrm: Apocalypse, Infinite Requiem, and Hope.

Following the Silurian fiasco, the Doctor picks up a distress call from an alien trapped on the Earth, and decides to take care of the problem himself without involving the Brigadier. The Brigadier becomes suspicious of the Doctor’s surreptitious activities and assigns Sergeant Purvis to spy on him -- and Purvis finds proof that the Doctor is indeed engaged in something he doesn’t want the Brigadier to know about. Liz finds herself caught in the middle when the Brigadier sends UNIT troops to the site the Doctor was investigating, thus preventing the Doctor from getting to the stranded alien. Infuriated, the Doctor continues trying to solve the problem on his own, but the Brigadier refuses to stand by doing nothing, particularly when villagers begin dying from epileptic seizures. The alien is being protected by the local parish priest, but its attempts to communicate telepathically with the villagers have inadvertently resulted in their deaths. The alien flees into the woods when the Brigadier attempts to capture it, and when it tries to return to the church it finds UNIT troops blocking the way and tries to scale the walls of the building. Confused and desperate, it tries to communicate telepathically with the soldiers blocking its way, and to prevent a mass slaughter the Doctor has no choice but to shoot and kill it.

Time-Placement: The pressing emotional issues around the decision to entomb the Silurians is still very much on the Doctor's mind, so it probably takes place between Doctor Who and the Silurians and The Ambassadors of Death.

The Doctor and Sarah are on vacation at the ruins of Phaester Osiris when they find the body of archaeologist Edwin Carver clutching a familiar scarab gem -- the Eye of Horus. The Doctor sends Sarah back to the TARDIS while he visits Carver’s hotel room, but while leaving he is kidnapped by members of the Cult of the Black Pyramid. Sarah avoids the cultists pursuing her, and a beggar who witnessed the Doctor’s kidnapping tells her where can be found (in fact, the beggar is a Time Lord in disguise, here to ensure that they do not lose their most promising agent). Disguised as a cleaning woman, Sarah breaks into the room where the Doctor is being held by the cultists’ leader, Anwar Nazir. Nazir claims to have taken Sarah prisoner as well, and although the Doctor knows he is lying, he hands over the scarab anyway to see what will happen. Sarah helps him to break out of the hotel room, and they follow Nazir to the Black Pyramid, where Nazir intends to awaken the sleeping Horus. The Doctor tries to warn Nazir that Horus was a monster who played with civilisations as a child plays with toys, but Nazir ignores him and puts the scarab in place -- and since the Doctor had secretly scratched it earlier, it short-circuits, incinerating him. Horus turns out to have been dead for centuries due to a fault in his life-support system, and the energy released by the short circuit destroys the Black Pyramid.

Time-Placement: They Doctor and Sarah seem to be taking this particular trip because of the events in Pyramids of Mars, so I've placed it directly after it.

The Doctor visits the mines of Alexandria, looking for gold with which to make a ring for Susan’s wedding, but he and Barbara are separated from Ian by a cave-in. The slaves and guards seem to recognise Barbara as their Queen, and as she and the Doctor are taken to her husband Ptolemy they realise that history has been changed. Barbara meets the real Queen, who turns out to be an older version of herself, while the Doctor visits the Library and learns that it has been fitted with temporal baffles which enable patrons to collect books from the future. Barbara goes to the library to look for the Doctor, but accidentally passes through a temporal baffle and ends up nine years in the past. An alien spaceship has just crashed in the bay, and the confused and angry citizens are rioting. Barbara is beaten by an angry mob and loses her memory, but retains the connection to the TARDIS which enables her to understand the alien Rhakotis when he cries out for help. She is thus able to translate for him, and over the next nine years, Rhakotis helps Alexander and his successor Ptolemy to build an empire while Ptolemy and the amnesiac Barbara fall in love and marry. But some refuse to accept Ptolemy as Alexander’s successor, and nine years after the crash civil war breaks out. Despite Rhakotis’ warning that his repairs are still not complete, Ptolemy forces him to raise his ship from the sea and strike down his enemies. As the ship rises from the sea Queen Barbara sees it, finally regains her memory, and rushes to the library just as the rebel army arrives. Ptolemy and a rebel soldier strike each other dead at the same time, and Barbara realises that the soldier was Ian. Rhakotis’ ship explodes, destroying Alexandria -- but the Doctor emerges from the temporal baffles with a book from his own home world, which somehow ended up in an Earth library. He gives Barbara and Rhakotis the option of using it to undo the damage they have caused, and they agree to do so, erasing this alternate history -- even though this means Barbara loses her husband and family, and Rhakotis loses his life in the crash.

Time-Placement: Ian and Barbara are the only companions, therefore the story must take place between The Dalek Invasion of Earth and The Rescue. It must also be set directly after Venusian Lullaby because it is mentioned at the end of that book that the Doctor would like to find some gold to make a wedding ring for Susan, and he still thinks about it at the beginning of this story.

Continuity Note: The book from the Doctor’s homeworld is called The Ancient and Worshipful Law of... and though the Doctor never actually finishes speaking the title, it’s most likely ...Gallifrey, from Shada.

The Doctor and Peri arrive in the medieval village of Sair, which is experiencing peace and prosperity even in the midst of drought. While Peri visits the taverna and drinks with the beautiful young man Tabilibik, the Doctor explores the town and comes to suspect that the villagers possess incredible psionic powers. Peri, bored by Tabilibik’s posturing, leaves him to go find the Doctor -- but, angered by her rejection, he casts a spell of Fascination upon her, and she immediately falls in love with him. The Doctor discovers that the elders of the town have been using witchcraft to ensure their people’s survival, but Tabilibik is abusing his powers and is turning Peri into his devoted slave. The Doctor alerts the elders to Tabilibik’s abuse and breaks the spell, and he and Peri depart, leaving the elders to punish Tabilibik for his crimes.

Time-Placement: Between Planet of Fire and The Caves of Androzani. Peri has been travelling with the Doctor for months, so likely set after Erimem departure.

The Doctor, Steven and Dodo take a holiday cruise to the planet Bukol, but when they try to pass through customs, someone else’s face appears on the Doctor’s holographic visa -- and Steven and Dodo suddenly denounce the Doctor as an impostor. Inspector Yerma locks up the Doctor and searches the liner, and the “real” Doctor -- the Sixth Doctor -- is found unconscious in the garbage hold, having been beaten and left for dead. He is taken to the hospital to recover, but is attacked by the mysterious Mykloz, a shape-shifter who disguises himself as an orderly and tries to poison him. Meanwhile, the First Doctor escapes from custody and tries to speak with Steven and Dodo, but they refuse to explain themselves and threaten to turn him in again if he continues to harass them. The First Doctor eventually runs into an old friend who provides proof of his identity, and the Sixth Doctor, having survived Mykloz’s attack, disappears from hospital when the real Steven and Dodo escape from the liner where they had been confined all this time. Mykloz attempts to kill them, but the Sixth Doctor intervenes and Mykloz is taken into custody. Mykloz is an assassin from a race of xenophobic shapeshifters, the Maleans, and is hunting two fugitives who had developed the ability to empathise with other species. The Sixth Doctor was helping them to escape to an extra-dimensional Sanctuary through a gateway on Bukol, but when Mykloz attacked him, the two fugitives, alone and helpless, disguised themselves as Steven and Dodo in the hope that the First Doctor -- who was unaware of the presence of his future incarnation -- would get them through customs. Mykloz, however, switched the Doctors’ visas, and the fugitives were forced to denounce the First Doctor to avoid being arrested themselves. The Sixth Doctor helps the fugitives into the Sanctuary, but Mykloz escapes from custody and tries to kill them again; however, when he fires his blaster into the closing gateway, he opens a dimensional rupture and is expelled to a random location elsewhere in space and time.

Time-Placement: All the stories between The Ark and The Savages are directly connected. There's however a break at the very end of The Gunfighters, so we have to assume this story takes place in the gap. The 6th Doctor is travelling alone, so his segment is set somewhere between Killing Ground and Business Unusual.

The Time Lords transport the Doctor into Earth’s future to pick up a message capsule intended for Liz Shaw. With the help of the Doctor’s alien scientific knowledge, the future Liz has founded a power cadre of scientific elite and has reshaped the world along purely rational lines; when this timeline’s Doctor protested, he was placed in cryogenic suspension, his mind linked to the TARDIS console’s telepathic circuits so his knowledge would continue to serve mankind. The former members of UNIT who refused to join the Power Elite now fight them from an underground base in London. The Doctor is kidnapped and tortured by Mike Yates, but Yates has been compromised by his enemies and unwittingly leads the Power Elite’s security forces to his base. In the confusion, the Doctor escapes and makes his way to the SunTrap, a solar power reservoir built by the Power Elite; there, he meets Liz, who has come to believe that the SunTrap is malfunctioning. In fact, Director Helios of the SunTrap turns out to be a Solarian, one of the last survivors of the race which was destroyed when the Time Lords detonated their home star to create the supernova which first gave them the power of time travel. Helios intends to guide the human race towards a new destiny and use them as an army with which to invade Gallifrey and destroy the Time Lords. The Doctor destroys Helios and returns to present-day Earth, where he gives Liz the message capsule. Inside the capsule Liz finds a CD-ROM recording of her own mind, which she had made in the future, and when she sees what she and her dreams are destined to become, she agrees to put her knowledge to different uses.

Time-Placement: This story is set just after Liz has technically left UNIT, placing it between Inferno and Terror of the Autons.

The Doctor, Tegan and Nyssa arrive in a research station which has been abandoned after an attack by guerilla terrorists, and discover that the cyclotron is still operational. The Doctor and Nyssa analyse the odd readings coming from the cyclotron, which seem to indicate that there is a disembodied consciousness within the acceleration ring itself. When Tegan unexpectedly begins to channel the spirit of a dead woman named Kate, the Doctor realises that for some reason Kate has been trapped inside the cyclotron. He programmes the TARDIS to travel to the moment that Kate entered the cyclotron -- the only moment at which she can escape again -- and leaps into the cyclotron to rescue her. Kate has been trapped by the laws of physics, endlessly reliving her own life and capable of visiting any moment in it, but unable to change them. As a Time Lord, the Doctor is able to halt the flow of Time as Kate experiences it, but she refuses to leave with him and instead tries to change the past so she will never go to the Base in the first place and have to suffer through the terrorist attack and her endless life in the cyclotron. Her attempts to change history damage the Time Vortex and threaten to destroy the Universe, and the Doctor therefore deliberately places himself in a life-threatening situation; in order to save his life, Kate has no choice but to exit the cyclotron with him. They escape in the TARDIS as the terrorists burst into the room, and the Doctor returns her to Earth, to pick up the rest of her life where she left off.

Time-Placement: The fifth Doctor, Nyssa, and Tegan are still arguing about Adric's death and the possibility of going back to rescue him, showing the recentness of Earthshock. But it is an old argument, repeated many times before, so it's probably set later in the season, after the return of Tegan in Arc of Infinity.

As the stories are told, it becomes apparent that Allison’s client is the Doctor -- one of him, at any rate -- but they seem no closer to finding out what he was doing in L.A. Allison, however, has come to certain conclusions of his own after seeing his client’s reluctance to let Silverman touch the Bukolian visa and his utter refusal to let him touch a newspaper reporting recent UFO sightings -- not to mention the fact that the Doctor described in the stories has a great respect for life, while Allison’s client nearly murdered Silverman’s bodyguard. Allison therefore takes his client out to the town mentioned in the newspaper report, holds him at gunpoint and demands to be taken to the real Doctor. As he had suspected, his client turns out to be the shapeshifting assassin Mykloz. A flying saucer suddenly appears over the town, and Mykloz overpowers the surprised Allison and takes him to his hideout, where Allison finally meets the real Doctor. The Maleans are invading Earth, but Mykloz found that he was developing empathy for the human race. He tried to correct the mutation with a genetic stabiliser, but the Doctor stole it and hid it somewhere in L.A. -- which is why Mykloz wanted Allison to retrace his steps. Allison helps the Doctor to escape, and the Doctor rigs the hideout to self-destruct, destroying the approaching Malean saucer and putting an end to the invasion.

Time-Placement: The Doctor is described as wearing his brown coat and question mark pullover, so it would place the story before White Darkness, where the Doctor changes his outfit. And as the real Doctor only calls out to Benny at the end of the story, that would put it somewhere between Love and War and Deceit. Also, in Highest Science's prelude, the Doctor is going through a bunch of newspapers when he finds evidence of a Fortean Flicker... which starts the events of the novel going. In Playback, the Doctor says that he found out about the story's villain by reading a newspaper report, quite by chance. So I think perhaps one could assume the Doctor found this report in his varied collection of newspapers, and that after the events of Playback he returned to them and found the Fortean Flicker.