Charley cowers away in hiding as the Doctor, or Zagreus, storms through the TARDIS, alternately screaming threats and begging for help. Charley struggles to understand what’s happening, but suddenly finds herself on Harley Street with her mother, on the way to the doctor’s surgery. Lady Pollard chastises Charley for daydreaming, and blames the tendency on Charley’s favourite book, Alice’s Adventures in Wonderland -- a book with an odd inscription from her “Nana Saviltride” suggesting she might enjoy this divergence from her ordinary books on etiquette. Charley thought she’d lost Alice at school some time ago. Though she can’t quite recall how she got here, she’s becoming aware that something odd is going on, particularly when her mother transforms into a white rabbit while speaking to Dr. Zagreus’ receptionist. The door to the doctor’s office won’t open at first, which suggests that someone is trying to keep Charley away from the doctor -- but then the door does open, revealing a familiar figure whom Charley recognises as Brigadier Lethbridge-Stewart.

The TARDIS opens up doors for the raving Doctor, who is still unsure whether he actually is the Doctor or Zagreus, and eventually leads him to the library. There, the Doctor leafs through the books which are falling from the shelves, and finds a copy of A Brief History of Time with all of its pages blank, as if its history has not yet been written -- or as if it’s been erased. A familiar but almost inaudible voice then whispers through the library, offering cryptic advice and clues to the Doctor’s plight. In his madness, the Doctor cannot recognise the voice of his third incarnation, but he soon realises that his Ship is trying to help him. The voice leads him to the top shelf, where he finds The Alice Compendium -- the only book which still contains words, although the Doctor has trouble making out certain words in its inscription. He then finds a secret passageway with a light at the end of the tunnel, and for a moment, his mind clears enough for him to be appalled by what he’s done to Charley. He also realises that the voice is a projection of the TARDIS, but the weakness of the projection implies that most of his ship’s power is being diverted elsewhere -- perhaps to help Charley.

With the Brigadier prompting her, Charley recalls the devastating events in the universe of anti-Time, and the Doctor’s subsequent madness. The Brigadier explains that Harley Street was a holographic projection generated by the TARDIS out of Charley’s own memories, and as he does so, Charley finds herself transported into another historical projection; this time, her mother is confronting the head of Charley’s boarding school, Miss Lime, demanding to know how Charley managed to slip away from the school without being noticed. As Charley watches, she is taken aback to realise just how much her mother respected her independence. She then finds herself back aboard the TARDIS, where the Brigadier explains that the damaged ship is creating these holo-projections so that Charley may observe historical events which may have some bearing on whatever has happened to the Doctor.

The passageway from the library leads the Doctor to a chamber containing a large glowing ball of something or another. Though he can’t identify it, his mind is starting to clear, and he theorises that this is the one part of the TARDIS still untouched by the anti-Time infection. His mind will remain clear as long as he remains in this room, and he is even able to hold a conversation with the Zagreus side of himself; but if he leaves this room, Zagreus will become dominant, and Zagreus, unlimited by the physical laws of this Universe, wishes only to destroy. Through Zagreus, the Doctor can see all of the parallel timelines that exist alongside this one, and according to Zagreus, they are all equally valid -- and all equally doomed if Zagreus is unleashed. If the Doctor stays here, he will remain in control of himself -- but he will be unable to rescue Charley...

Charley and the Brigadier find themselves in another holographic environment, this time an army barracks sometime in the 1950s. The Brigadier wonders aloud if this is where the Divergence occurred, and Charley finally realises that this is not the Brigadier at all, but a holographic avatar of the TARDIS itself, sent to help her investigate what’s happened to the Doctor. The Brigadier advises against seeking help from the Time Lords, lest they also become infected with the anti-Time inside the TARDIS. Instead, he and Charley must participate in these recreations of significant historical events to find out what’s happening; the people in the simulations will be given form and voice from the TARDIS’ memories, and will believe the Brigadier and Charley to be a part of the scenario. As the Brigadier speaks, young Captain Neil MacDonnell arrives and greets him and Charley, believing them to be a man from the Ministry and his driver -- who are here to see “the doctor” at work.

The Doctor returns to the library, calling out for Charley, but uncertain that he will be able to keep himself from harming her. As he struggles to keep control of himself, the voice of his third incarnation speaks to him, and again, The Alice Compendium falls to the floor. This time, he can read the words which were hidden from him earlier; one is Charley’s name, and the other is the word “divergence”. Also, he realises that the name of “Nana Saviltride” has a disturbing significance which completely escaped him earlier...

Captain MacDonnell shows the Brigadier and Charley to their quarters, but as soon as he’s gone, they slip out to investigate further. The Brigadier needs Charley to investigate for him, as he is insubstantial and cannot interact with his surroundings. They soon locate a storeroom full of crates marked “Top Secret”, and determine that this base is in Cardington -- perhaps coincidentally, this is where the R101 was launched from in 1930. Captain MacDonnell then arrives with his co-worker, Miss Foster, and though they’re surprised to find “Sir Geoffrey” and his driver in the room, the Brigadier reminds them that he’s been granted full access to the base. MacDonnell accepts this explanation, and asks Miss Foster to escort the Minister and his driver to the laboratory.

Once clear, Miss Foster reveals herself to be a Ministry secret agent, sent in undercover to investigate the possibility that the base has been infiltrated by a spy sent to find out about Dr Stone’s work. Out of the possible suspects -- Captain MacDonnell, base chaplain Matthew Townsend, and the reverend’s niece, Mary Elson -- Miss Foster has decided that Townsend is the most likely culprit. The discoveries Dr Stone has made seem to contradict his most cherished beliefs, yet despite his criticisms and their bitter arguments, Townsend still encourages her to continue with his work. Charley considers it only right to proceed with caution in any new scientific endeavour -- but as she speaks, the base is rocked by a tremendous explosion...

Even the Doctor feels the strength of the explosion, but he doesn’t know what caused it -- and fears that only Zagreus may be able to deal with it. Struggling to find his way back to the console room, he instead finds himself within a forest inside his own ship. In a clearing, he finds a tall metal box and a ten-foot-tall talking Cat which seems to have stepped straight out of Alice in Wonderland. At the Cat’s urging, the Doctor looks inside the box to find a bottle marked “Drink Me”, but the Cat tips him inside and slams the box shut, and the Doctor finds that the bottle contains cyanide. The Doctor pretends to suffocate and then informs the Cat that he’s dead, and since the Cat is still hearing his voice, that must mean that the Cat has gone mad. The Cat will have no way of knowing which is true until he opens the box to look for himself. The Cat allows the Doctor to suffer for a moment longer before opening the box, but the point has been made; the analogy to Schröedinger’s Cat is blatant enough for the Doctor to work out what’s happening to him. As long as he remains in the TARDIS, he is both the Doctor and Zagreus, but if he emerges, one or the other will become true...

The explosion in Cardington base was the sound of Dr Stone’s experiment running out of control, but she and Townsend manage to shut down the machine before any serious damage is done. The Brigadier and Charley arrive to find Stone flush with success, though Townsend seems in a less than celebratory mood. As Townsend takes the Brigadier and Charley to the mess hall, Stone secretly contacts “the Deputy Director” to confirm that everything is going according to plan. Captain MacDonnell then contacts Stone to confide that he’s worried about Miss Foster, and although he and Stone seem to be an item, Stone nevertheless advises MacDonnell to invite Miss Foster out to dinner and get to know her better -- “for King and Country.”

Stone then joins the others in the mess hall, where an old argument with Townsend breaks out afresh as the Brigadier and Charley watch. Townsend is an open-minded clergyman who believes that modern science may answer the questions which have plagued his faith for years. As the Brigadier listens to the argument, Charley speaks with Mary Elson, who is clearly fond of her uncle but doesn’t understand the details of his work; all she knows is that Stone’s project is code-named “Dionysus”.

At the Brigadier’s prompting, Townsend admits that he has serious reservations about Stone’s work, or rather its military applications. He does not wish to impede the progress of science, merely to ensure that it is conducted in an ethical manner. Stone mocks his religious beliefs, and as Townsend grows more frustrated, it becomes clear that he has become obsessed by his own doubts; he needs to understand why humanity has evolved into the form it has, and for what purpose. Was humanity designed by some form of alien life -- perhaps even by God? In his enthusiasm, he lets slip that he regards Mary as an obstacle in his path; he was forced to become her guardian when her parents died in a car accident, and his obligations to her have impeded his “important” work. Mary storms off in tears, realising how little her uncle really cares for her. Before following her, Charley lags behind to hear Stone reveal the military application for her project. Earlier tonight, Dionysus tore a hole in something, perhaps the very fabric of reality. What if they could do the same in the middle of Moscow?

Charley tries to comfort Mary, assuring her that her uncle just became over-excited and must truly care for her underneath. At that moment, Captain MacDonnell arrives, bleeding from a gunshot wound. Charley and Mary take him back to the mess hall, seeking help, but the argument has continued in their absence, and Townsend has now lost his temper with Stone. He refuses to let her turn her great work to violent ends, and, determined to prove himself, he storms off to the laboratory. The others trail along in his wake, as the wounded MacDonnell tries to deliver an important warning.

The Brigadier is already back in the laboratory, where he finds Miss Foster planting a bomb on the Dionysus project; the agent sent to search for the spy was the real spy all along, and once the prototype has been destroyed she will sell Stone’s work to the Communist rebels in Cuba. But before she can get away, Townsend bursts in, planning to operate the machine, tear a hole in the fabric of time and space and reveal the face of God. As Miss Foster holds them all at gunpoint, however, MacDonnell reveals too late that Miss Foster shot him after he learned she was a spy. Miss Foster orders Stone to activate the machine, threatening to shoot the non-essential personnel if she does not, starting with Mary Elson and then MacDonnell. Townsend takes little persuading, as he’d intended to activate the machine in the first place, but he refuses to be hurried -- and when Miss Foster tries to do so, MacDonnell takes advantage of her distraction to shoot her dead. But even with the immediate threat removed, Townsend powers up the machine instead of shutting it down. Charley turns to the Brigadier for advice, only to find that he’s no longer there...

In the forest, the Doctor realises that the Cat is an avatar created by the TARDIS to guide him while he tries to pull himself together. The word “divergence” in The Alice Compendium must be significant somehow, and the Cat reveals that it’s related to the explosion he heard earlier, the sound of a devastating event echoing throughout history. Something terrible is on its way, too powerful for either the Doctor or Zagreus to keep at bay. As the sound of the explosion echoes through the TARDIS once more, the Cat quote the nursery rhyme again: “for Zagreus is the end of the world...”

At the dawn of history, as the elite of Gallifrey take the first steps towards becoming Time Lords, Rassilon’s enemies are preparing to strike back against him. In the wilderness of Outer Gallifrey, Provost Tepesh of the Arcalian chapterhouse and his adjutant, the Lady Ouida, meet with the Grand Mother of an outlawed Sisterhood and her companion, Cassandra of the House of Jade Dreamers. Tepesh and the Great Mother would normally have little time for each other, but now they have a common enemy -- Rassilon, who has outlawed the Great Mother’s “superstitious” religion and has hunted Tepesh’s people nearly to extinction. However, Lady Ouida has found the secret hiding place of Rassilon’s Foundry, which he has hidden in the wastelands, shifted seconds into the future. Now, while Rassilon is back in the Capitol, his enemies will break in, learn his secrets, and turn them against him.

This is, of course, another holographic simulation, which Charley will soon be participating in. The Brigadier removed her from the last scenario just in time; in the real version of history, the Minister and his driver were killed as well. Now the Brigadier and Charley know the truth about the incident at Cardington; there is something outside the boundaries of space and time, and for a moment it nearly broke through. Charley and the Brigadier appear within Rassilon’s Foundry, and while waiting for the scenario to begin, Charley asks the Brigadier whether it’s possible for her to take the anti-Time infection into herself, saving the Doctor’s life. The Brigadier scoffs, and claims that the change is permanent; the Doctor will forever be Zagreus, and he can never be permitted to leave the confines of the TARDIS to spread the infection to the rest of the Universe. But Charley wonders; if this is the case, then why, when she was reconstituted from the dimensional rift, did Rassilon place her inside the TARDIS with the infected Doctor?

Bored and angry, the Doctor begins to chop down the trees in the forest, at least until the Cat points out that he’s doing so without an axe. The forest is an illusion, and that means that the act of cutting down the trees must be symbolic. The Doctor reasons out the truth; the Cat, an avatar of the TARDIS, is giving him cryptic hints about his situation because something else must be preventing it from helping him directly. And since the Doctor is able to think without being overwhelmed by Zagreus, this must mean that he never left the room with the glowing ball of matter. By cutting down the illusory trees, he is soon able to see this for himself. But was he placed here for his own protection, or just to keep him out of the way while something else was happening elsewhere? The Doctor finally realises the truth; his personality was split in two when he absorbed the anti-Time energies, and he wasn’t the only being to do so. The inscription in The Alice Compendium, “Saviltride”, is an anagram for “evil TARDIS”. The legendary Zagreus isn’t just the Doctor, it’s also his ship...

Tepesh, Ouida, the Great Mother and Cassandra enter the Foundry only to find Rassilon waiting for them inside -- although it’s actually Charley they’re seeing. Once again, the Brigadier vanishes, leaving Charley to muddle through the scenario as best she can. She realises just how dangerous a position she’s in when Cassandra says something which offends Tepesh -- and Tepesh has Ouida kill Cassandra and drink her blood. Charley is horrified, but realises that this is a simulation of ancient Gallifrey and asks the Great Mother why Cassandra can’t just regenerate. However, the Great Mother has no idea what this means, and when Tepesh and Ouida investigate, they find that Rassilon has been tampering with Gallifreyan physiology to enable his people to live after death -- a secret which until now has been exclusive to the Vampires.

As Tepesh challenges “Rassilon” to explain himself, an automatic recorder activates and asks the visitors if they wish to see more of the Foundry -- which already appears larger on the inside than the outside. Determined to learn all of Rassilon’s secrets, Tepesh demands more, and Charley takes the opportunity to request information on the Divergence. The response is horrifying. Rassilon has investigated the future, and has learned that within 10,000 millennia a race more powerful than even his Time Lords will evolve. In order to prevent this, he has sent self-replicating, biogenic molecules back in time to seed all habitable planets in the galaxy, thus ensuring that all intelligent life in the galaxy evolves into a form approximating the Gallifreyan norm. The creatures whose existence he feared will be trapped within their own, now divergent timeline, which Rassilon intends to seal off within a time loop; otherwise, it is possible that the Divergents could escape at the end of the Universe and create a new web of Time to supplant the one created by Rassilon.

Charley realises that the Dionysus Project temporarily broke the web of Time and allowed the Divergents a glimpse of the timeline which had replaced theirs -- and that she must now travel to the end of Time to find out whether the Divergents do manage to escape. The Brigadier then appears, satisfied that he’s learned all he needs to, but Tepesh sees him as Erata, the third member of the Vampires’ Committee of Three. His arrival seems to confirm that the Foundry is not as well protected as Rassilon’s ego would believe, but when Charley comments on Tepesh’s own ego, Tepesh nearly throttles her in a fit of rage. According to Tepesh, the Vampires were a peaceful people, drinking only the blood of genetically bred animals, until Rassilon found their world and decided that they were too different to be allowed to live. Only after his purges did the Vampires spread through the Universe, hiding in the shadows, taking on the forms of other races and drinking the blood of intelligent beings in order to survive. Now, Tepesh will have his revenge by exposing Rassilon for the xenophobic despot that he is.

Fortunately for Charley, Tepesh can’t afford to kill Rassilon until he’s learned all there is to know about the Foundry. Charley orders the Recorder to continue, and it reveals that the Foundry draws its power, not from the black hole now renamed Rassilon’s Star, but from energy siphoned out of the Divergent timeline. The Brigadier advises Charley to switch off the power, and she does so -- but the power drain weakens the reality lock between the timelines, and the Divergents begin to break through. As they do so, the Great Mother reveals what she’s always known; just as Rassilon has stolen the secret of regeneration from the Vampires he hounded to extinction, so the rest of the Time Lords’ technology was stolen from the Divergent timeline. The recorder then announces that the Foundry’s safety protocols have been activated; to prevent the Divergence from escaping, the entire facility will be firestormed. Tepesh and Ouida try to flee, only to find that the Foundry is now sealed off from the outside world and there are no air currents for them to ride to safety. The Brigadier vanishes, having learned all he needs to know from this scenario. It seems Charley is trapped with the others, but at the last moment, a mirror appears in mid-air, and Charley leaps through to safety as the Foundry is firestormed and Tepesh, Ouida and the Great Mother are all killed.

Charley finds herself in a control chamber; whoever she is in this scenario, there’s a receiver in her ear, and Corporal Heron is warning her that his troops are under attack. Looking for a way out, Charley stumbles into a hall of mirrors and is confronted by a six-foot-tall mouse in battle armour... which she soon realises is her own reflection. Three snarling pirates burst into the hall of mirrors and attack her, but at the last moment, she is saved by a giant duck who shoots the pirates and takes Charley, “General Mouse”, to safety in the 5-D theatre.

The Doctor challenges the TARDIS to face him personally, and uses their symbiotic link and the anti-Time energy to start blowing up rooms in its architectural configuration. The Brigadier materialises in front of him, and the Doctor, realising that he is an avatar of the TARDIS’ evil side, demands to know what’s happening to Charley. The Brigadier refuses to reveal what’s going on, and when the Doctor threatens to destroy more of the TARDIS, the Brigadier reveals that he can defend himself -- and summons a Jabberwock, straight out of the pages of The Alice Compendium, to attack the Doctor. The Doctor is forced to flee for his life as the Brigadier departs to keep an eye on Charley.

Charley has determined that she’s in a theme park of sorts, in which the animatronic animals are at war with animatronic humans -- pirates, miners and astronauts. Captain Duck sets off to rescue Corporal Heron, while Sergeant Gazelle leads Charley to the movie theatre to address her troops. Today’s battle has gone poorly for the animals; the enemy has taken the turnstiles, Waterfall Mountain and Deep Canyon Adventure. On Sergeant Gazelle’s advice, Charley orders her troops to retreat to Cosmic Mountain and try to hold off Goldilocks’ army while she and Gazelle revive the Animator. As she tries to cope with this surreal situation, it occurs to Charley to wonder why there are no visitors to this theme park.

Captain Duck reaches the turnstiles only to find that Corporal Heron’s troops have fallen. She is then confronted by Goldilocks and the fairy Tinkle, who sprinkles magical fairy dust over Duck, brainwashing (or reprogramming) her to switch allegiances. Duck contacts Gazelle, who informs her that General Mouse is leading the animal army to Cosmic Mountain -- but the animals don’t realise that Captain Dodo has fallen to Tinkle’s magic dust as well, and that he will be able to fly Goldilocks and her allies directly to the Mountain, bypassing the battle entirely. Of course, since this is another holographic simulation, the animatronics see him as Captain Dodo, and not as the Brigadier.

Charley and Gazelle arrive in the Animator’s chamber to find that he is an ordinary human in suspended animation. Before they can revive him, Goldilocks and her allies arrive and capture them; however, it seems that they too want to revive the Animator. Charley thus does so, and the Animator proves to be a cheerful, jolly man named Walton Winkle, known throughout the Earth Empire as Uncle Winky -- until his heart condition forced him to enter suspended animation on 18 December 2367. Uncle Winky assumes that a cure for his condition has been found and that Winkle’s Wonderland is open for business once more, but the animatronics reveal that it has been relocated several times since Winkle entered suspended animation -- and it is now located on the dead world once known as Gallifrey.

Goldilocks orders Tinkle to sprinkle her magic dust over the animator, but Gazelle shoots the fairy, and Duck then shoots Gazelle. Winkle is horrified by the violence, and Goldilocks takes sadistic pleasure in informing him that there are no children in his wonderland -- or anywhere at all. Winkle has been in suspended animation for 60 billion years, and all the children in the Universe died out long ago. As Winkle weeps for the loss of innocence, Charley realises that Cosmic Mountain is now built over the location where the Foundry once stood, and that the animatronics have fallen under the influence of the Divergence. Their animatronic paws and hands are too clumsy to operate the machinery themselves, which is why they’ve been fighting to reach Uncle Winky -- so he can destroy Cosmic Mountain and thus break open the reality lock, allowing the Divergents to emerge into the real Universe at last.

It seems that Winkle has nothing to live for, but despite his despair, when Goldilocks urges him to destroy Cosmic Mountain, he instead activates his merchandising protocols. To ensure that his creations could not be sold to a third party who would dilute their charm by using them for advertising purposes, Winkle planted microchips in each of his animatronic creations, and only he knows the codes. He now switches them all off. However, Charley realises that the Divergents intended to escape just as the Universe came to its end, and that is now occurring. Uncle Winky collapses, as they never found a cure for his condition after all, but Charley supports the dying man outside to witness the end of the Universe. Winkle is horrified to see the wasteland that has become of his wonderland, and as the sky tears open above them, he too sees the Divergents trying to force their way out from the other side of the rift. However, they are too late; Winkle dies, and the Universe comes to an end before the Divergents can escape from their own timeline.

At the last moment, the Doctor plucks Charley out of the simulation and back into the TARDIS console room. He has escaped from the Jabberwock and regained some hold over his sanity, much to her relief -- but then the Brigadier appears in the console room, and Charley realises that she can’t trust either him or the Doctor. The Doctor tries to warn her that the TARDIS itself has become Zagreus, but the Brigadier scoffs and informs him that this is not the case. It is the Doctor who is to become Zagreus; the TARDIS’ destiny is quite different. Rassilon appears in the TARDIS to confirm the truth; the Doctor and Charley lay unconscious for six months after the anti-Time explosion, and in that time, Rassilon contacted the TARDIS and offered to purge it of the infection called the Doctor in exchange for its help. The Brigadier followed Charley through the historical simulations in order to make up his mind, and he has decided to do as Rassilon asks. The TARDIS opens its doors and casts the Doctor’s most prized possessions out into the Time Vortex... as well as Charley. The Doctor is unable to intervene, for fear that if he gets too close to the doors and falls out, he will unleash Zagreus upon the Universe. Now Charley is lost to him, and Rassilon is in control of the TARDIS...

In the Presidential quarters on Gallifrey, Romana is dictating a children’s book to K9 when she receives an emergency message from Cardinal Braxiatel in the Watchtower. Though the Doctor’s TARDIS has been kept under quarantine and close observation, it has somehow vanished without dematerialising of its own accord. Romana confirms that her Presidential transducer emitter is still in place, and prepares to investigate; however, before she can do so, the savage Leela breaks through her defence systems to convey a message which she received in a dream. Romana is initially sceptical until Leela describes the old man who gave her the cryptic message; it appears that Rassilon has chosen to communicate telepathically through Leela with news of the Doctor, and Romana understands where she’s being told to go next.

Romana, Leela and K9 transmat to Rassilon’s tomb, where Leela takes the ring from Rassilon’s body despite Romana’s warnings. The spirit of Rassilon then possesses Leela, using her as a medium so his attempt to communicate with Romana will not be recorded in the Matrix. Leela uses the ring to open up a hidden door in the tomb, and Romana follows her through, despite K9’s warning that he is detecting “non-standard” Matrix pulses.

Charley explains to her companions that they are not the people they believe themselves to be, but recreations constructed from Zagreus’ memories and given the forms of the Doctor’s former incarnations. They are the only three people in all of history to have seen the Divergence, and the TARDIS doesn’t want the Doctor to know about it, which is why it has expelled them from its body. Convinced that their arrival here is no coincidence, Charley insists that they visit Rassilon’s tomb, but Tepesh believes that they are here to play the Game of Rassilon, and he refuses to participate. Before he can find somewhere to hide, however, he and the others are confronted by the Jabberwock, which has also been expelled from the TARDIS. Charley and Townsend recite the poem Jabberwocky, trying to remember the creature’s weakness, and Winkle notices that the creature becomes subdued when poetry is recited. He, Townsend and Charley improvise their own nonsense verse, and thus convince the Jabberwock to fly them to the Dark Tower.

Romana, Leela and K9 pass through a mirror which vanishes into thin air to find themselves in a Matrix simulation of the Dark Tower as it was in ages past. Rassilon has laid out a sumptuous meal for his guests, but Romana turns down the invitation to dine when K9 reveals that this sealed sub-Matrix is in fact composed of cloned brain tissue. Rassilon thus gets straight to business and presents Romana with resignation papers, instructing her to pass on her authority to her successor, Zagreus; otherwise, the possessed Leela will slit her throat. Romana refuses to co-operate, but the papers were merely a side issue. Rassilon already has what he wants -- his ring. Leela was the only one on Gallifrey whom Rassilon could possess without setting off alarms in the Matrix, and only the President could get her past the security systems around the Dark Tower. Rassilon takes his ring and departs, and the possessed Leela strikes off K9’s head, leaving him unable to defend Romana as Leela goes after her with a knife.

Tepesh tries to direct the flight of the Jabberwock, but succeeds only in crashing into the Tower. Leaving the unconscious monster behind, Charley and the others enter the Dark Tower, where they find their way blocked by a booby-trapped chessboard. The voice of Rassilon recites a riddle, and Townsend, Tepesh and Winkle all conclude that the answer involves the number pi. However, when Winkle tries to cross the board using the number as a grid reference, he is nearly skewered by a bowspike, and Charley realises that the riddle’s mention of circles was a red herring; the real solution has to do with another line in the riddle, about the movement of a knight. Charley and the others cross the board, and then investigate a distant commotion to find Leela attacking Romana; this is not the real Dark Tower after all, but the sub-Matrix simulation. Charley knocks Leela out with a vase to the head, and explains the situation to Romana as she understands it. Rassilon clearly intends to use the Doctor for his own nefarious purposes -- and if the Doctor’s friends can’t rescue him, they will have to kill him.

Rassilon has given the TARDIS avatar in the Brigadier’s form a corporeal body made of agitated protoplasm, and the avatar has chained up the Doctor in a dungeon and is preparing to torture him. The Doctor warns the avatar that Rassilon will not keep his promise to set it free, but then realises that, if Rassilon would never risk unleashing anti-Time into the Universe, this must mean that the doors did not open onto the real Time Vortex. He demands to know what’s happened to Charley, but the Brigadier flies into a rage. The TARDIS has been the Doctor’s oldest and most loyal companion, and the Doctor sacrificed it without a second thought in order to save the life of a foolish Earth girl who should never have survived in the first place. The Doctor realises, to his surprise, that the TARDIS is actually jealous of Charley.

Rassilon then summons the Doctor and the Brigadier to the Foundry, which is separated from the rest of the Universe by a reality lock and is thus safe for the Doctor to enter. This is where the greatest artefacts of Time Lord history were constructed, from the statue of Nemesis to the D-Mat gun. This is also where Rassilon stores any perceived threat to his web of Time, including a solar system which he has frozen in Time to prevent it from becoming the home of a species which would have threatened the supremacy of the Time Lords had they been allowed to exist. Though the Doctor does not realise it yet, the Divergence is stored in another of these vaults. Rassilon then leads the Doctor to the Foundry’s smelting works, where the Doctor is unable to intervene as the Brigadier avatar drops the police box shell of its former self into the cauldron, melting down what was until now the only constant in the Doctor’s life.

Charley pleads with Romana to spare the Doctor’s life, but to no avail. Meanwhile, Uncle Winky somehow manages to repair K9, who momentarily mistakes him for the Doctor. Tepesh’s Vampire senses detect a hidden mirror nearby, and K9 confirms that the nearby wall is an illusion. Leela is the first through, and the others follow, leaving K9 to guard their backs. They find themselves in the first level of the Foundry, where the dusty remains of the real Tepesh still litter the floor. Townsend cracks the logarithmic code which opens up the door to the next level of the Foundry, but only after he has done so does he realise that the inscription was written in Old High Gallifreyan. This confirms Charley’s growing suspicions, as she’s noticed that Tepesh, Townsend and Winkle have been displaying familiar knowledge and abilities. When the TARDIS created the historical simulations, the characters within were given shape from its own memories -- and as well as the Doctor’s physical appearances, Townsend, Tepesh and Winkle have acquired some of his memories and personality traits as well. In essence, they have become aspects of the Doctor.

The Brigadier arrives with orders to keep the others away from the Doctor, but Charley, Leela and Romana hold him off while Townsend, Tepesh and Winkle get past. They find the Doctor by an anvil deep within the Foundry, chanting the Zagreus rhyme as he hammers out a sword from the special ores and anti-Time extracted from his melted-down TARDIS. Rassilon seems triumphant; the destruction of the TARDIS has shattered the Doctor’s sanity, and he is now convinced that he is Zagreus. Before he can kill Townsend, Tepesh and Winkle, however, they reveal the truth; Rassilon is manipulating him to rid himself of the Divergence. Until now he has only been able to keep them trapped, but when the Doctor chose of his own free will to give himself up to anti-Time, he became the very weapon which Rassilon needed. Once all trace of the Doctor’s former self has gone, Rassilon intends to send Zagreus into the Divergent timeline to destroy every last one of the Divergents with his anti-Time blade. The Doctor realises that he’s to be used to commit genocide, but as he tries to resist, Rassilon takes the blade from him and cuts down Townsend, Tepesh and Winkle. The Doctor, weak and alone, struggles to resist as Rassilon calls on him to assume the mantle of Zagreus.

In the smelting works, Charley and Romana distract the Brigadier, who empties his gun at them -- but as Leela charges him he reveals that the gun, like himself, is a construct of weird matter, and it contains as many bullets as he needs. He shoots Leela and turns on the others -- but Romana is now close enough to use her transducer emitter, which she took for safekeeping after checking on it earlier. She now uses it to transport the Brigadier into the crucible, where he melts down just as the rest of the TARDIS did earlier. Charley sets off to find the Doctor while Romana checks on Leela; fortunately, she’s only suffered a flesh wound. As they set off after Charley, they fail to notice something rising from the crucible behind them...

Charley finds Rassilon gloating as the Doctor struggles to maintain his sanity. Knowing that he will soon be overwhelmed by the Zagreus side of his personality, the Doctor gives Charley the anti-Time sword and begs her to kill him before he is lost forever. Rassilon stands by, amused, believing that Charley could never kill the man she loves -- but he has miscalculated, for Charley now knows that the Doctor would not ask her to kill him if he loved her in return. Leela and Romana arrive too late, and before they or Rassilon can stop her, Charley takes the sword and stabs the Doctor, breaking down in tears as she does so.

The dying Doctor finds his fifth, sixth and seventh selves waiting for him in his subconscious, but there is no blinding flare of regeneration this time. To his shame, the Doctor realises that his mind was so muddled by the anti-Time and by Charley’s anger that he actually wanted to die. But he also realises why he’s seeing his past incarnations now. When Rassilon stabbed Townsend, Tepesh and Winkle with the anti-Time blade, it drew the missing parts of him out of them -- and when Charley stabbed the Doctor with the same blade, those parts were restored to him. Now that he can think clearly again, he knows that Rassilon must be stopped from using the anti-Time blade against the Divergents -- and that he doesn’t want to die. The moment for regeneration has passed, but Zagreus has the power of anti-Time; if the Doctor gives in to this side of himself, he can cancel out the moment of his death.

Thus, though Charley stabbed the Doctor, it is Zagreus who wakens. Rassilon, delighted, urges Zagreus to take the anti-Time blade and strike down the Divergents for the sake of the history he knows. However, Romana steps in, reminding him that all things pass; the nature of history is change, and it is not their position to stand in its way. Rassilon scoffs, and insists that Zagreus use his great powers. That’s just what Zagreus intends to do, but not on Rassilon’s terms. He will not be a dictator’s puppet. Before Rassilon realises what’s happening, Zagreus seizes him and drags him off to the vaults to face his destiny. Leela and Romana stop Charley from interfering as Zagreus opens the reality lock and casts the screaming Rassilon into the Divergent timeline to face the creatures whose timeline he has supplanted.

Zagreus then turns on Charley, Leela and Romana, but the Brigadier unexpectedly arrives and overpowers him. When the Brigadier avatar was cast into the crucible, all of the melted-down parts of the TARDIS were reunited -- except for the anti-Time blade, which the Brigadier now absorbs into himself. Complete once more, and free of the anti-Time infection, the Brigadier gives Charley a vial marked “Drink Me”, which she forces the Doctor to drink. The vial is an aspect of the glowing ball of light which the Doctor found earlier, which had also taken on the forms of The Alice Compendium and the Jabberwock; it is pure zero matter, which counters the anti-Time infection, and the sane part of the TARDIS has been trying to give it to the Doctor in a form which its evil side would not recognise.

The Doctor’s mind is now stable, and the TARDIS is as good as new. All Charley wants to do is put these traumatic events behind her and set off on another exciting adventure through space and time... but she’s stunned when the Doctor tells her that this will not be possible. Though the zero matter has stabilised him, he is still infected with anti-Time, and if he steps beyond the safe confines of the TARDIS or the Foundry then he will spread the infection through the Universe and destroy all he holds dear. He thus intends to travel into the Divergent Universe and try to find a place for himself there. Charley insists that he needs her by his side now, more than ever, but he screams at her to leave -- or was that the Zagreus side of him?

Heartbroken, Charley storms out of the TARDIS, but Romana, who’s been lurking in the shadows and watching it all, knows that the Doctor drove Charley away for her own good. Romana has remained to deliver a warning, but the Doctor already knows what she’s going to say, and he no longer cares. All of his childhood heroes have let him down; Omega, Morbius, Borusa, and now Rassilon himself. How long until the power of the Presidency corrupts Romana as well? He is about to enter a new and unfamiliar universe, one without the Time Lords, but he’s quite looking forward to that. Romana delivers the warning anyway; the Doctor cannot be allowed to spread the infection of anti-Time through the Universe, and if ever he tries to return, the Time Lords will be waiting to stop him. Romana bids her old friend goodbye, and the Doctor’s last request is that she find a place for Charley in the timeline he’s leaving behind.

Outside, Leela finds Charley trying not to cry -- not for herself, but for the Doctor, whom she knows needs a friend by his side in this troubled time. She already knows what she intends to do, and Leela understands. When Romana emerges from the TARDIS, only Leela is waiting for her. As the TARDIS dematerialises, taking the Doctor out of this Universe forever, Leela and Romana mourn the passing of a hero. Romana then inquires after Charley, and Leela admits that the TARDIS has a back door. Despite herself, Romana is impressed.