The President of Gallifrey is charged with High Treason for seeking to lead his people into a war of conquest. He is therefore deposed and sentenced to permanent exile. Vice-President Saran will become the new Acting President until the next elections, although well aware that the ambitious Junior Cardinal Borusa has his own eye on the position. The former President departs from Gallifrey, but vows to return...

For some time, Peri Brown has been leading a team of freedom fighters on the planet Sylvana, and she’s found that she has a knack for jungle fighting. However, the unpredictability of her techniques eventually becomes predictable, and one day she leads her team into an ambush. All but two of her fellow guerrillas are killed, and she and the survivors, Gina and Kyrin, are brought before Commander Nadir of the local garrison. Nadir orders the young lieutenant Hakon to treat the prisoners with courtesy until they are shot at dawn; however, later that night the camp is attacked by the forces of the Alliance, and the hot-headed Hakon decides to shoot the prisoners immediately. Peri and Kyrin overpower him, but not before Gina is shot and killed. They lock Hakon up in their cell and attempt to escape, but he gets out of the cell, tracks them down and shoots Kyrin. Before he can shoot Peri, the Alliance ships land, and Peri shoots him first while he is distracted.

Peri returns to Nadir’s office, where she sees the Commander surrender to the Draconian High Commander Aril, the Sontaran Battle-Major Streg, and their Ogron footsoldiers. Aril and Streg inquire after the guerrilla leader named Peri, and are surprised when Peri presents herself. Aril takes Peri aboard his battle cruiser and flies her to the flagship of the Alliance fleet, where she freshens up and awaits an audience with the leader of the Alliance, the Supremo. She watches from an antechamber as the Supremo addresses the assembled forces of the Alliance; representatives of every civilised species in the galaxy, up to and including the Cybermen, all hang on his every word as he chastises them for their failures and congratulates them on their successes. He is in all ways the perfect military leader, and it’s clear that his soldiers would die for him. The Doctor has changed a great deal since Peri last saw him...

One year earlier: Moments after stepping out of the TARDIS on a supposedly peaceful planet, Peri is attacked by a flying predator which nearly takes off her arm before the Doctor can kill it. The Doctor places Peri in stasis and takes her to the one place where she can get the treatment she needs -- the Hospice on Karn, home of the greatest surgeon in the galaxy, Dr Mehendri Solon. The Doctor gets to Solon by quoting the Pact of Rassilon to the Hospice’s advisor, the Reverend Mother Maren, and convinces Solon to treat Peri by shamelessly claiming that only a man of his genius can save her life. Solon performs the operation, but doesn’t care whether Peri survives the complications; all that matters is that he has proven his skill by reattaching the severed nerve endings in her arm. Impressed by himself as always, Solon then retreats to his private laboratory to continue his secret experiments...

The Doctor hopes to slip away as quickly as possible without damaging the web of Time, but he’s detained by the head of security, Commander Aylmer Hawken, who wishes to know how this stranger managed to slip past all of the Hospice’s defenses. The Hospice is an neutral oasis of peace in the centre of a galaxy at constant war, and some of the warring factions would do anything to rob their enemies of the care the Hospice provides. However, Maren has warned Hawken to treat the new arrival with courtesy, and after speaking with him, Hawken decides to trust him. The Doctor identifies himself simply as John Smith, dropping the title “Doctor” so Solon won’t be suspicious when they meet in the future. Meanwhile, Maren returns to the Temple of the Flame; despite the pact, she fears that the arrival of a Time Lord is a bad omen, marking great danger to come.

Hawken discusses the mysterious “Smith” with Lord Delmar, who is officially the owner of the Hospice -- although he acknowledges that the aristocracy’s time has passed and therefore acts in a purely advisory capacity. In that capacity, he advises Hawken to tread carefully, for he suspects that Smith is one of the mysterious Time Lords of legend. He also tells Hawken that some of the outer planets intend to form an alliance to protect themselves against the larger empires of the sector, and advises him to let them hold their peace conference here in neutral territory. Hawken agrees, and tells the Doctor about the conference, which is apparently the idea of a charismatic new warlord called the General. The Doctor is vaguely interested, but no more, as he still intends to leave before he interferes in anything significant.

Peri is making a fine recovery, although Solon warns that there’s a possibility her body may still reject the new neural linkages. This doesn’t seem to be happening, but she does have a problem -- Solon’s assistant Drago, whose bedside manner is far from appropriate. The Doctor gently but firmly threatens Drago with a formal complaint, and later that night, Peri hears Drago complaining to Solon and suggesting that the Doctor and Peri be killed. Solon dismisses his fears and returns to work on “Project Z”, and Peri, concerned, follows him and Drago to a secret panel in the hallway outside. She tells the Doctor, who refuses to take an interest and tells Peri that she shouldn’t get involved. She ignores his advice, distracts Drago, steals his key and slips through the secret panel -- where she discovers that Solon has been stitching together the corpses of various different species. When one of the patchwork bodies comes to life and grabs her, she pulls away -- and the zombie’s hand comes off at its wrist, still clutching hers.

Repulsed, Peri returns to her room, where she pries the hand from her arm and shows it to the Doctor. However, he’s irritated with her for disobeying him, and orders her not to interfere any further. He intends to return the hand to Solon and say no more about it -- but Solon has already discovered that someone has interfered with his experiments, and he has Drago inject Peri with a “vitamin supplement” -- in fact a toxin. He then informs the Doctor that Peri’s body is rejecting the new neural linkages, and that only the Elixir of Life can save her. The Doctor knows that this is a ruse; nevertheless, he has no choice but to go to the Temple and beg Maren for a vial of the Elixir. Fortunately, she is in a good mood, and she gives him what he needs and has the other Sisters psychically transport him back to the Hospice. There, Solon pretends to administer the Elixir to Peri, but in fact simply injects her with the antidote and keeps the Elixir for himself. The Doctor later confronts him, admits that he wasn’t fooled, and warns him that he’s left a letter with Hawken to be opened in the event of his or Peri’s deaths. Solon might be able to talk his way out of trouble nevertheless -- but how long would Drago last under interrogation?

Satisfied that he’s given Solon something to think about, the Doctor decides to go once Peri has fully recovered. Unfortunately, the delegates for the peace conference arrive, and Hawken becomes fully occupied with security matters; thus, the Doctor can’t get through to him and ask permission to leave. Delmar then invites the Doctor and Peri to the conference reception, as he fears that he will get no good conversation from the delegates, who all appear to be thugs. The delegates behave themselves at the reception, but the Doctor recognises the predatory glint in their eyes and identifies them as Gaztaks -- space mercenaries and pirates, the dregs of the galaxy. When the General enters the room, there is a moment of near-recognition between him and the Doctor, but both shield their minds from the other. The General speaks privately to Solon, who considers himself the General’s most loyal servant, and then obliquely warns “Smith” to keep out of his business. The Doctor realises that the General himself must be a renegade Time Lord, up to no good.

Hawken also mistrusts the General, and decides to bug the peace conference. He invites the Doctor to listen in, and the Doctor agrees but sends Peri off to keep her safe. Irritated by his patronising attitude, Peri nevertheless sets off shopping, only to run into the General on his way to the peace conference. The charismatic General stops what he’s doing simply to talk to her, and, charmed, she accepts his invitation to dinner. The Doctor and Hawken, however, are unaware of this, and they don’t know who the Gaztaks are talking about when they coarsely discuss their General’s latest conquest and hoping that he’ll pass her over to them when he’s finished, as he has with his others. The General himself then arrives, and although the sound breaks up, the Doctor builds a device to help break through the jamming signal... and it soon becomes clear that the General and his Gaztaks are in fact conducting a war council, and are planning to conquer the rest of the civilised galaxy.

Disturbed, the Doctor departs to ponder what he’s learned, and runs into Peri -- but when she tells him she’s having dinner with the General he flatly forbids this. This is the wrong move, as Peri furiously stands up for her right to make her own decisions. The Doctor repeats what he overheard at the conference, but Peri points out that the way the General’s subordinates talk doesn’t necessarily indiate how the General himself may behave. Knowing that he’s handled the situation badly, the Doctor nevertheless asks Hawken to arrest Peri on trumped-up charges in order to keep her out of the way; he knows she’ll never forgive him, but believes that he must do this for her own good.

The General orders his troops to attack the Temple and steal the Sisterhood’s supply of Elixir; the Sisterhood will then stockpile more for themselves, but the General’s army will return and take it all. Hawken sends his security guards to arrest the General and his men, while the Doctor sends a telepathic message to Maren warning her of the danger. The Sisterhood use their psychic powers to start a rockslide and crush the approaching Gaztaks, while the General and his men retreat to their ships and flee. Unfortunately, the General refuses to abandon his latest conquest -- and he thus kidnaps Peri on his way out. Hawken is unable to prevent the General from escaping, and as he goes, he deliberately drops his mind shield to let the Doctor know who he really is. He’s going by the name of Rombusi, but the Doctor knows him as Morbius.

Peri finds herself trapped on Morbius’ flagship, facing the fate worse than death which the Doctor had warned her about, but although she briefly considers suicide she soon comes up with a better idea. When Morbius arrives, she has scraped patches of her skin raw with a plastic knife, and she claims that they are symptoms of a highly contagious infection she picked up from the predator’s saliva. As she had hoped, Morbius is far too vain to risk being infected himself, and he despatches her in an escape pod with enough food for three days. Fortunately, she is picked up by a freighter from Sylvana, but as the war begins in earnest she is unable to get word of her survival through to Karn. She must start a new life for herself on Sylvana, but eventually the neighbouring planet Freedonia allies itself with Morbius’ army and invades Sylvana on his behalf. Eventually, Peri can tolerate no more of their oppression, and when she hears a group of would-be guerrillas discussing some poorly thought-out plans to strike back, she chimes in with some suggestions of her own...

The Time Lords must be warned of the danger posed by Morbius. The Doctor thus admits to Hawken and Delmar that he is himself a Time Lord, and volunteers to return to Gallifrey -- but as in this era he is still a fugitive, he must go incognito as an ambassador from Karn. Delmar lends the Doctor his private space yacht for the journey, while Hawken prepares to defend the Hospice against Morbius’ inevitable return and Maren retreats to the Temple. Meanwhile, Solon returns to his work; with the Elixir provided by the Doctor, he has completed his research, and when Morbius returns to Karn, Solon intends to present him with an army of the dead.

The Doctor lands on Gallifrey, and attempts to convince Saran and Borusa of the danger which Morbius poses. They are unwilling to take responsibility for him until Councillor Ratisbon of the Celestial Intervention Agency arrives with proof of the Doctor’s true identity. The Doctor insists that the fact that he risked returning to Gallifrey proves how seriously he regards the threat, and after some deliberation the Time Lords reluctantly agree to deal with Morbius. He must be defeated by a military action to prevent him from becoming a martyr; thus, the great empires of the galaxy will have to unite in one alliance to take him down. Convincing them to work together requires an ambassador with great imagination and experience of alien cultures, who is unafraid to take risks... and only the Doctor is qualified. He has no choice but to accept the assignment. He thus visits the Emperor of Draconia and the Sontaran Battle-Marshal Skrug, and both agree to fight for his cause, as their own forces were recently attacked by Morbius’ army. Or so it seems; in fact, the Doctor correctly suspects that Ratisbon in fact staged these attacks in order to make his job easier.

Ratisbon assigns Ensign Vidal of the Chancellory guard to act as the Doctor’s personal aide, and supplies the Doctor with a flagship suitable for the Supreme Co-ordinator of the Alliance. The first war council takes place on the desert planet Aridus, but there are arguments from the start; the Sontaran Battle-Major Strug favours a direct frontal assault while the Draconian High Commander Aril prefers to stage a series of diversionary attacks. The Doctor realises that neither approach will work until they have more forces at their disposal, and suggests following in Morbius’ footsteps, liberating the planets he has conquered one by one. Every time Morbius conquers another world he must leave troops behind to occupy and subdue it; thus, every victory weakens him, while every time the Alliance liberates a planet they will become stronger and will be well-practiced when the time comes for the final battle.

The first planet conquered by Morbius is Fangoria, and this is thus the first planet which the Alliance liberates. The Gaztaks left the Mayor, Makir, as a puppet ruler by threatening his family, but when the Alliance frees the hostages and reunites them with Makir, the grateful Mayor pledges to give the Alliance all the support they need. Vidal, greatly moved by Makir’s display of gratitude, admits that Ratisbon planted him here to keep an eye on the Doctor -- but from now on Vidal will serve him loyally. As their campaign continues, different species begin to argue over who should serve as the Doctor’s personal bodyguard, and to stop the arguments he eventually chooses the Ogrons. Honoured by his choice, but unable to pronounce the title “Supreme Co-ordinator,” it is the Ogrons who first dub him “Supremo”. More species join the Alliance, including Cybermen and Ice Warriors; at one point the Doctor even has a nightmare in which the Daleks offer their support. And so the war continues, until eventually the Alliance reaches Sylvana and the Doctor is reunited with Peri at last.

The Doctor and Peri share stories, and the Doctor admits that he’s found himself enjoying his new role in life. Thousands of soldiers are willing to obey his every command, he’s fighting for a just cause, and he appreciates the intellectual challenge of warfare -- but he knows that he’s in charge of a war in which innocent people are dying. Peri feels drawn to this new, tortured version of her friend, but the Doctor -- while apparently tempted -- turns down her implicit offer. The next day, the Doctor receives word that Morbius has finally stopped moving forward and is entrenching his position, finally preparing to fight the Alliance. The last battle will take place on Karn, as Morbius intends to seize the Sisterhood’s stockpiles of the Elixir. His fleet is already on its way -- and unbeknownst to the Doctor, Morbius has sent out special orders to the rest of his army, taking a desperate gamble which should ensure victory. However, the Sisters sense the evil approaching their Temple, and use their psychic powers to destroy the mercenaries he’s sent to attack them.

Enraged, Morbius orders his fleet to bombard the Hospice from orbit. The Alliance fleet then arrives, and to his young navigator’s amazement, the Doctor calculates a short hyperspace jump and successfully materialises his fleet between Morbius’ forces and the planet. Morbius’ fleet is taken by surprise and retreats, and the Alliance forces land on Karn, knowing that they will next face Morbius’ army in a ground battle. Maren is waiting when the “Supremo” emerges, and he tries to convince her that the Sisterhood must join forces with the Alliance -- but despite his warnings, she remains arrogantly convinced that the Sisterhood can protect itself.

Morbius’ army lands, and a pitched battle breaks out. Due to Morbius’ irrational loathing of non-humanoid life forms, his entire army is composed of human mercenaries, and the cosmopolitan composition of the Alliance army thus strikes a psychological blow. Nevertheless, the Alliance forces find themselves losing -- until Maren reluctantly recognises the truth in the Supremo’s words and orders the Sisters to attack. The confusion spread amongst the mercenaries by the Sisterhood’s psychic attacks enables the Alliance to gain the upper hand -- but just as the battle appears won, a second wave of mercenaries arrives. Morbius has recalled all of his forces from the planets they still occupied, sacrificing his empire in the short term in order to win this battle and crush the Alliance once and for all.

The Sisters have exhausted themselves, and Morbius, secure in his victory, calls a temporary ceasefire in order to gloat. As another wave of ships approaches, Morbius contacts the Supremo and his battle leaders and offers them a chance to surrender; they refuse, knowing that Morbius would have them tortured and executed. Morbius returns to his lines, and the battle resumes -- but just as all appears lost, the occupants from the latest wave of ships arrive and attack Morbius’ men from behind. President Makir of Fangoria has finally assembled an army of his own from the planets which the Alliance has liberated, and Commander Nadir of the Freedonian army is on his side. Freedonia’s governing officials allied themselves with Morbius out of greed when he promised them eternal life via the Elixir; once Nadir learned the truth he staged a coup and now fights for the right side. Morbius’ army is crushed, and the General himself is captured trying to escape.

Morbius will face public trial and execution here on Karn. Victory has not come cheaply; Streg suffered fatal wounds while throwing himself atop a laser cannon aimed at his Supremo, and Taro, the young navigator of the Doctor’s flagship, also joined the battle and died for it. The Time Lords have no interest in these matters, and prepare to take charge -- but it soon becomes clear that the army owes its allegiance to the Doctor, and not to them. The Doctor insists that they deal with the welfare of his troops before they discuss Morbius, and Saran, Borusa and Ratisbon realise that they’ve either created a monster or the best leader Gallifrey ever had. Morbius is imprisoned in the Hospice, while the victors celebrate -- but during the night, a pale, cloaked figure is spotted in the corridors of the Hospice, and some of Hawken’s security guards are found dead, their bodies drained of blood. Grimoire, Morbius’ vampiric second-in-command, is still on the loose...

Morbius is placed on trial before the tribunal of Borusa, Saran and Ratisbon, and although he refuses to acknowledge the court’s authority, it nevertheless finds him guilty and sentences him to vaporisation. Before he can be removed from the courtroom, Solon’s army of zombies bursts in and attacks; he was unable to revive them in time to join the battle, but he still hopes to save Morbius. However, his creations are dismal failures, and the occupants of the trial chamber discover that they can pull the poorly-stitched zombies apart with their bare hands. Morbius and Solon are imprisoned separately, but the Doctor knows that he’ll have to free Solon to ensure that the future unfolds as he’s already seen it.

That night, the Doctor heads for Solon’s cell only to find that Grimoire has beaten him to it, seeking an ally to help him free Morbius. The Doctor thus nips ahead to the execution chamber, and orders his Ogron bodyguards to take away the protesting technicians. He then confronts Morbius alone, injects him with an anaesthetic and hides as Grimoire and Solon enter the room. Grimoire is appalled to learn that Solon intends to remove Morbius’ brain and transplant it into another body so that nobody realises Morbius has escaped. When Grimoire tries to stop him, Solon decapitates him with his electric saw, and then removes Morbius’ brain from his body and stores it in a portable cryogenic unit. Once Solon has gone, the Doctor places Morbius’ body in the vaporisation chamber, and when Maren and the Time Lords arrive he distracts Borusa and rushes the execution before anybody has a chance to examine the body. Borusa presses the button which disintegrates Morbius’ body, and the Time Lords depart, satisfied. Maren knows that Morbius was already dead, but the Doctor claims to have administered a lethal injection, desiring to see Morbius die at his hands. Maren accepts his claim.

The next day, the Alliance forces hold a funeral for Streg and a dress parade for the Supremo. Saran, Borusa and Ratisbon offer the Doctor the chance to return to Gallifrey, but he knows that they have their own agendas for him and the Alliance -- and he and Peri slip quietly back to the TARDIS and leave before the Time Lords realise. The separate members of the Alliance return to their empires, and the Hospice is abandoned, as nobody has the heart to rebuild it. Karn itself is abandoned, apart from the Sisterhood, who shelter in their Temple, growing ever more fearful as their sacred Flame begins to die and their stocks of Elixir dwindle. Solon hides in the ruins of the Hospice, continuing his work, vowing to restore Morbius to life. And then, one dark and stormy night, a curly-haired stranger and his young friend arrive on Karn...