The Fifth Doctor and Turlough unexpectedly land in late 21st century Moscow after picking up on a serious problem with the Web of Time. Turlough tries to stay behind in the TARDIS until they somehow magically land on the planet of sunny beaches and pretty girls, but the Doctor drags him along nonetheless. Upon exiting, they find that a cult known as the Somnus Foundation has gained serious traction in Russia and set up a massive tower in the middle of Moscow - one with architecture native to the 51st century.
Turlough soon meets his Girl of the Week in the form of a young woman named Lena - and then has to rescue her from a Somnus thug. As it happens, her brother Alexi has just joined the cult, and she clearly doesn't trust the "Sleepers" with his safety; Lena and her best friend Pavel — a conspiracy geek — explain that the group promises its members enlightenment and utopian future, but are clearly involved with something unpleasant. After narrowly saving Lena from a psychic assassination attempt via a flock of angry birds, the Doctor decides to investigate further... by simply showing up at the Somnus Tower for a public tour. Unfortunately, Alexi has already been rewarded with a "True Name" and now seems to possess a different personality - one called "Great Seo"; now one of the leaders of the cult, he has no interest in leaving.
Worse still, cult founder Great Qel seems to recognize the Doctor: though she allows him to leave unharmed, she's clearly keeping an eye on him. A Time Lord is exactly what she needs, and she seems to be holding a grudge against this one in particular. Pavel later reveals that Qel used to be a respected scientist by the name of Natalia Pushkin, and the Somnus Foundation was just a research group - up until the day their clinic burned down.
Curious, Team TARDIS, Lena and Pavel head off to ten years before - the day of the fire and the day Natalia renamed herself Qel. Confronted with the idea of time travel, Lena runs off really fast, crying about how she has to get to a hospital to stop her mother from dying - but is eventually talked out of it by Turlough. Meanwhile, Pavel and the Doctor infiltrate the Somnus clinic and find a group of human test subjects linked together via a Hive Mind; with a little technical help, the tormented hive mind explains that the alien being known as Qel has taken over the real Natalia Pushkin's body, and is trying to link the entire human race into a psychic singularity. Thanks to the Doctor's assistance, the experimental hive mind is able to commit suicide, setting fire to the clinic in the process. Unfortunately, the Doctor accidentally cuts himself on a broken window while escaping - allowing Qel to get a blood sample and recognize Time Lord interference in her experiments.
Shortly after Team TARDIS arrive back in the present, Lena has a breakdown over the lack of progress, coming within inches of handing the Doctor and Turlough over to the Sleepers before the Doctor manages to placate her. Eventually, she explains just why she tried to change the past: her mother had been suffering from terminal cancer on the night of the fire, and after witnessing all the suffering she'd been made to endure over the last few months, Lena took action; using the blackout that resulted from the experimental hive mind's suicide as cover, she switched off her mother's life support and "let her sleep." From then on she had to raise her brother on her own, but was so desperate to keep him safe that she ended up smothering him, destroying their relationship and driving Alexi to join the Sleepers.
Unfortunately, while Lena is busy explaining this to the Doctor, Qel is able to track down the TARDIS via the blood sample she took over a decade ago, and sends out a capture team to retrieve it - abducting both the TARDIS and Turlough, killing Pavel in the process. As it turns out, the cult leaders and its "enlightened" members are creatures from the far, far future, who plan to use the bodies of humans as their new host forms in order to escape the Heat Death of the Universe: their regular bodies in the far future are dying and barely kept together with bits of metal and flesh, as Turlough finds out when his body is stolen and he ends up imprisoned on Ember, the last surviving human outpost at the end of time - alongside earlier victims of the Somnus like the real Alexi and the real Natalia.
The next stage of the plan soon becomes apparent when the Somnus are able to extract the power they need by torturing the TARDIS, psychically linking the population of Moscow into another hive mind. After Lena succumbs to Despair Event Horizon and is assimilated into the gestalt, the Doctor is left to confront the cult leaders at the tower alone. There, Qel finally reveals what her race is: the very last humans in the universe.
In the future, the Time Lords saw the end of the universe approaching and gathered up all the races they considered worthwhile, before departing for a new dimension; humanity was left behind to die along with the burned-out stars. The Somnus Foundation's true goal is to transmit their brethren into new bodies into the past and escape the end of the universe; they've chosen a time just before human space colonization begins en mass, so it has the largest concentration of humans - allowing them to link enough minds together into a singularity capable of achieving psychic transubstantiation, a godlike gestalt powerful enough to rewrite history.
Meanwhile, in the future, Turlough is able to rally the transplanted victims enough to lead an attack on the Somnus power source keeping the hive mind stable; in the present, the Doctor uses the confusion that results as a means of playing up the rivalry between Qel and Seo long enough to distract them while he sabotages their machinery. As a result, the singularity breaks down, the Sleepers are evicted from their stolen bodies, and their victims are finally allowed to return home, reuniting Lena and Alexi. However, with the tower exploding around them, Natalia realizes she can't let Qel return to the future or else she'll just start her mind transference experiments all over again; trapping the Somnus founder inside her consciousness, she remains behind to die in the collapsing tower while the Doctor and the others escape.
In the far future, the Doctor visits Seo, the very last human in the entire universe — not to stop humanity from dying out, but simply to be there when it happens and to pay his respects.
- Aliens Speaking English: The Doctor and Turlough get confused for Brits, because of the way they talk. The TARDIS's Translator Microbes make everybody else speaking English, though.
- Always Save the Girl
- And Then What?
- Assimilation Plot
- Badass Boast: Turlough gets in a magnificent one.
- Bedlam House.
- Bizarre Alien Biology: Turlough's body isn't suited at all for the cold. England is bad enough, but being in Moscow is pretty much hell for him.
- Break Them by Talking: See also Divided We Fall.
- Call-Back: Lena tells Turlough he has something of the wolf in him. He tells her she has no idea.
- Call-Forward: Turlough says he's got family out there, but no means of contacting them. The Doctor replies with "Ye of little faith." and the story ends with the two going, by Turlough's wish, "Somewhere warm!"
- Chronic Hero Syndrome: Turlough, despite being a perpetual case of The Complainer Is Always Wrong, goes out of his way to save a girl being assaulted by a guard.
- Cold-Blooded Torture: The TARDIS is tortured so hard, Five can feel it.
- Computer Voice
- Conqueror from the Future: The Sleepers.
- Conspiracy Theorist: Pavel in a nutshell; he's rather bemused to discover that's he's been more or less right, and that he's been working alongside aliens for the last hour or so, but other than that he takes everything in stride.
- Continuity Nod: Among the conspiracy nut's photos is a picture of a Yeti.
- Creepy Crows: See also The Swarm.
- Divided We Fall: The Doctor starts sowing seeds of discord as soon as he faces the The Man Behind the Monsters. To buy him time to get to the MacGuffin.
- Dying Vocal Change: In her final moments before the Somnus Tower explodes, Great Qel shifts wildly between her own voice and Pushkin's voice.
- Earth Is the Center of the Universe: A randomized Negative Space Wedgie makes the TARDIS end up on ... Earth.
- Eternal English: It's implied, but never stated outright, that late 21st century Moscow speaks English with a Russian accent.
- Evil Tower of Ominousness: The Somnus Tower, easily the tallest building in all of Moscow.
- Fantastic Racism: The Time Lords saw the end of the universe coming and took several species but not humanity.
- For Doom the Bell Tolls: The Sleepers' mind-transferal experiments cause major distortions in the fabric of space-time, most of which seem cause the bell in the local clock tower to ring repeatedly.
- For Inconvenience, Press "1": Lena's attempt to betray the Doctor is foiled by the Somnus Foundation's phone service, which doesn't allow her to speak to anyone but an answering machine offering free aura readings and consultations.
- Gas Leak Cover-Up: After Stuff Blowing Up a Russian News Reel says a terrorist attack involving hallucinogens caused people to start seeing things.
- Goodbye, Cruel World!
- Gratuitous Russian
- Humanoid Alien: When told he looks just like humans, Turlough snaps back humans look like him.
- The Doctor, at the end of the story, says there's plenty of aliens on Earth. Like the tall fellow with the blue hair.
- Humans Are Psychic in the Future: The Doctor says this will happen at one point, but in the story it's too early.
- Last of His Kind: Seo gives us a Tannhauser Gate speech and pleads the Doctor to Save the Villain. But it's too late.
- Left the Background Music On: MUSIC OFF.
- Natural End of Time: The Somnus' plot is driven by trying to escape this.
- Nice Hat: Turlough wears a Usanka at one point in an attempt to disguise himself. It doesn't work.
- Nice Job Breaking It, Hero!: The Doctor's interference at the clinic gives Qel everything she needs to enact the final stage of her plans.
- Internal Homage: Pavel mentions N-Space, in reference to the Third Doctor Radio Dramas episode "The Ghosts Of N-Space".
- Noodle Incident: The Doctor's not allowed back into the Kremlin.
- The Reveal: The citizens of Ember are the last humans.
- San Dimas Time
- With just a slight dash of Year Inside, Hour Outside. A day equates to several weeks.
- Save the Villain: The Doctor tries to invoke this to Qel. It doesn't work out.
- Shout-Out: Rigel VII is mentioned as an Earth colony.
- The Stars Are Going Out
- Spot of Tea
- The Swarm: The Doctor, Turlough and Lena are beset upon by a swarm of Creepy Crows.
- Talking Your Way Out: How the Doctor gets Lena out a pickle. And how he eventually saves the day.
- Title Drop
- What Have I Become?: Alexi and Turlough are not happy with being trapped in the bodies of the future humans.
- Whole Plot Reference: To Neon Genesis Evangelion. Plenty of references are made to the "instrumentality of mankind" (which means exactly the same here as it did in the anime series) and to its "death and rebirth".