While visiting his friend Professor James Rafferty in Oxford, the Doctor detects a temporal disturbance and takes Ace back to the TARDIS to investigate. To his surprise, the TARDIS flight logs indicate that the ship has just returned from a 24th-century space station on the other side of the galaxy. As the Doctor sets off to retrace the journey, Ace hears the cloister bell tolling and sees a ghostly image of an armoured soldier -- but the Doctor sees neither warning, and he realises that this alternate TARDIS, plucked from a timeline in which his third incarnation died and given form by Ace’s memories, still does not trust him. When he and Ace arrive on station Q4 they find that the entire crew has aged to death, apparently within seconds. A rescue team arrives in response to the station’s distress call, but strange forces are still at work within the station, and two of the rescue party are killed by a mysterious energy wave. The other troopers find and arrest the Doctor and Ace, but as Lieutenant Commander Quallem prepares to take them back to the Icarus for interrogation, the rescue team detects an approaching energy source which they are unable to identify. The station’s bridge fills with a miasma of sparkling light which envelops and absorbs the Doctor, and the TARDIS vanishes, returning to Oxford and shifting into a different time frame to avoid detection.

Benny has remained in Oxford, where one of Rafferty’s students, Tom Cheynor, volunteers to show her around the town. As they drink at a local pub Tom notices a blonde woman staring at him; she departs without speaking to him, and nobody recognises her as the assassin who recently killed a man in Terminal Two of Heathrow Airport -- which is hardly surprising, as this will not happen for three days yet. Rafferty notices the blonde woman, Amanda, observing the lawn of St Matthew’s College, and when he questions her she reveals that she knows of his connection to UNIT, announces that there is a temporal anomaly on the lawn, and demands to be taken to Dr Styles, the college President. The President is in fact a renegade Time Lord named Epsilon Delta, who has set up a number of different aliases for himself on Earth, and Amanda is one of his most advanced android creations. Meanwhile, Benny and Tom return to Rafferty’s office, where they are attacked by a miasma of sparkling lights. They escape from the trap, and Tom, shaken by his experiences, departs as Benny tells Rafferty what happened. On his way home, however, Tom is picked up by Amanda.

Captain Romulus Terrin of the Icarus crosses over to Q4 to investigate in person, but he too is absorbed by the lights which attacked the Doctor. Despite the objections of Second Officer Darius Cheynor, Quallem detaches from Q4 and retreats to a safe distance to send a call for backup. As they depart, they receive a pre-recorded message from Q4, made over a week ago and held in storage for this moment. The picture quality has badly degraded, but the message is clearly a warning from the Doctor, telling the crew of the Icarus to change course at once. Before they can respond, the mysterious energy field appears again, and envelops the Icarus -- and the crew find themselves under attack.

The Icarus’ medical officer, Mostrell, completes his analysis of the human remains found on Q4, and determines that they appear to have been bombarded with tachyons; it’s as if something was using Time itself as a weapon. Just as he is dismissing this as foolish speculation, the ghostly Time Soldiers phase through the Icarus’ hull and attack the crew. Mostrell is transformed to a baby by a glancing blast, but Ace and Lieutenant Strakk, pursued into the ship’s game room, defeat their pursuer by using a mirror to turn the Soldier’s tachyon beam upon itself. Cheynor, realising that Quallem can’t deal with the situation, relieves her of command, but he has acted too late; the Icarus has fallen. As the Time Soldiers take the bridge, a skeletal figure swathed in darkness materialises on board, and begins to torture Cheynor, demanding the access codes for the ship’s warp motors.

Terrin and the Doctor have been transported one week back in time, and are aboard Q4 before the attack which will destroy it. They are charged with trespassing and questioned, but co-ordinator Helena Vaiq comes to believe that they are telling the truth -- as far as they believe it. When a technician is found aged to death in an isolated corner of the station, the Doctor has no choice but to show Vaiq proof of his claims -- the desiccated ID of station commander Ballantyne, which the Doctor took from his dead body in one week’s time. Vaiq allows the Doctor to record a message for the Icarus, warning them to turn aside from their course -- for he knows what they are fighting, and it’s a creature which thrives on temporal paradox. According to Time Lord legend, the Garvond is the embodiment of all the evil of the Time Lords’ minds, given form by the Matrix -- but when the Doctor first heard the legend of the Garvond, he realised that his own mind was part of it, and erased his mental print from the Matrix to prevent it from ever existing. Somehow, this act of the Doctor’s has been removed from history, and the Garvond has been born; but since the Doctor is a part of it, he was able to negotiate a path through the time distortion it had generated, and he and Terrin thus survived their passage through the Vortex.

Benny tries to locate the TARDIS and contact the Doctor, but her homing device directs her to the apparently empty lawn of St Matthew’s College. Rafferty recalls the blond woman’s odd claims, and takes Benny to confront the President, who locks them both up with Tom Cheynor. Despite his brilliant mind, Epsilon Delta was stuck in a series of menial jobs on Gallifrey, until he followed the Doctor’s example, stole a TARDIS and fled to freedom. Filled with bitterness against those who had failed to recognise his potential, when contacted by the Garvond he leapt at the chance to serve it in exchange for power and revenge. The President takes his TARDIS to Q4 and sends Amanda to capture the Doctor and Terrin, and once they are all together he explains that Amanda has already travelled forward in time to assassinate a minor government official. This has changed history, and when the flow of Time corrects itself, the energy, once channeled through the proper Time Focus, will give the Garvond the power it needs to restore itself fully.

Ace and Strakk are captured by the Time Soldiers and taken to the bridge, where the Garvond ages Quallem to death and threatens to do the same to the rest of Cheynor’s crew until he gives it the information it needs. Cheynor has no choice but to do so, and Ace realises that the warp engines must be functioning for the Garvond to take the entire ship through Time. She, Strakk, Cheynor and a soldier named McCarren create a distraction and get to the engine room, where McCarren tries to guard the others’ backs while they disable the warp engines. The engines, however, have already been possessed by the Garvond, and McCarren’s weapons prove useless against the Time Soldiers. The security systems turn on Ace and the others, and the Time Soldiers kill McCarren and take the others back to the bridge. There, the Garvond punishes them by forcing them to relive their greatest fears and doubts, and in so doing, Ace realises that she does not trust the Doctor to do the right thing.

The Time Soldiers materialise in the President’s TARDIS, and he transports them and his prisoners back to St Matthew’s College. The Doctor has no choice but to summon his own TARDIS back to the proper time frame in order to save his friends’ lives -- and by delivering the Doctor’s TARDIS to the Garvond, the President has served his purpose. Much to his surprise, he and Amanda are then deleted from history, as the government official whom Amanda assassinated turns out to have been the President himself in another of his aliases. The Doctor takes Benny and Tom with him, telling Tom only that he is no longer safe in Oxford, and leaving Rafferty and Terrin behind. As soon as Tom steps out of the TARDIS on the Icarus, however, he is possessed by the Garvond, and is revealed to be the Time Focus; the two time zones where the Garvond is active are connected through Tom and his descendent Darius. The Doctor meekly gives in to the Garvond’s demands and allows it into the TARDIS, and the infuriated Ace follows them in -- but she finds herself and the Doctor in an unfamiliar part of the TARDIS. Before boarding the Icarus the Doctor reconfigured the internal structure of the TARDIS to separate them from the Garvond -- but it is searching for them, and they must find the TARDIS library before the Garvond finds them.

Rafferty and Terrin return to the President’s TARDIS and programme it to retract its most recent journey back to Q4. An energy field has just been detected approaching the station, and within the field Terrin recognises the shape of the Icarus. The Time Soldiers are preparing to channel their power through the Icarus’ weapons systems, thus using the Icarus itself to cause the disaster it was sent out to investigate, and providing the Garvond with another paradox to feed on. But as the Time Soldiers work, Strakk tells Benny about the Time Soldier which was destroyed with its own weapons, and she manages to send a message to Q4 in Morse code -- an antiquated system which only Rafferty can understand and translate. He passes on the message to Vaiq and Ballantyne, who realise that by increasing power to the asteroid deflection shield they can temporarily turn it into a giant mirror. There is no time to rig a remote drone for the work, however, and Terrin gives his life to do so by hand, knowing he will be incinerated when he makes the final connection. He completes his work just as the Time Soldiers open fire -- and the energy is reflected back to its source, destroying them.

The Garvond tracks the Doctor and Ace down to the TARDIS library, but it is distracted for a vital second when its soldiers are wiped out, and the Doctor separates it from Tom and traps it within a dimensionally transcendental Gallifreyan book, The Worshipful and Ancient Law of Gallifrey. He disposes of the book within a dimensional pocket, trapping the Garvond forever. He then transports the Icarus and its surviving crew back to their proper place in Time, and takes Tom and Rafferty back to Oxford. Ballantyne never sent out the distress call which summoned the Icarus in the first place, but this is a minor paradox which the Doctor is sure will easily be resolved. But Strakk is aging at an accelerated rate due to his exposure to the Time Soldiers’ weapons, and has only ten years of life left. Ace blames the Doctor for not seeming to care that people fought and died on his behalf, and Benny, sensing their growing antagonism, begins to wonder whether she really wants to keep travelling with them. The Doctor, however, has more important things on his mind. He knows for a fact that he erased his mind-print from the Matrix, and the fact that the Garvond nevertheless came into existence means that an event in his past has been changed. The enemy who created the Silurian Earth has struck again -- and this time, has successfully altered the flow of Time in the real Universe…