A fleet of unidentified warships possessing incomprehensible technology has laid siege to Gallifrey and is ignoring all attempts at communication. Commander Vansell of the Celestial Intervention Agency arrives in the Capitol in a specially modified Type 70 TARDIS, with urgent news for the Lord President. The siege of Gallifrey has been brought about by a change to history, and before their monitoring posts went down, the Agency detected the Doctor's artron signature within the time distortion...

The cloister bell begins to toll as the Seventh Doctor potters about in the console room. Upon hearing a distant, ethereal sound almost like a voice, he finds himself setting the destination co-ordinates without understanding why. The Time Lords attempt to contact him with a warning, but their transmission is cut off, and the Doctor, hearing the ethereal voice outside, sets off to explore. He finds himself in an alien swamp, and hears a young woman, Elenya, calling desperately for help in the distance; while following the sound of her voice, he stumbles across an unpleasant, cackling old hag who refuses to help and tells him that soon he and the girl will both be dead. The Doctor locates Elenya and saves her from drowning in quicksand, but when he takes her back to the TARDIS for warm, dry clothes, he finds that the key will no longer fit in the lock. Elenya claims to be the only survivor of a geological field trip; their ship stumbled across this uncharted world, was drawn into its gravity well, and broke up due to some sort of atmospheric distortion. Elenya was the only survivor. The Doctor finds her strangely familiar, but before he can pin down where he's seen her before, he and Elenya hear another ship crashing in the distance.

Elsewhere, a crippled old man named Sancroff passes the time by sniping verbally at his gaoler, the old hag Ruthley. Despite his apparently mild attitude she loathes him and hates having to tend him, and when she reports to the bored Commandant at the distant prison control, she claims that there have been no visitors to their world -- when in fact several ships have recently crashed into the planet's defense shield. She refuses to discuss the crashes with Sancroff, who believes they are indications that the shield is failing; she tells him only that nobody is coming to rescue him, and packs him off to bed. Once he's out of the way she contacts the leader of a bio-assassin squad and informs him that four ships have penetrated the shield successfully. The bio-assassin cultures within will activate upon impact, and at last Ruthley will be free...

The Doctor spots a lighted window about half a mile away, but as he and Elenya try to reach it, two more ships crash nearby, endangering their lives. The Doctor, wondering whether the pilots are suicidal or are making kamikaze runs for some greater cause, searches the wreckage of the nearest ship and finds what may be the gruesome remains of the crew -- but the "remains" appear to be growing, as if the creatures are not dying, but being born. Before he can investigate further, he and Elenya are captured by security robots sent to put out the fire from the ship. The Drudges report to Ruthley, who orders them to kill the intruders; that procedure is not permitted, however, and Ruthley doesn't bother to argue. The Drudges mind-scan the Doctor and Elenya to determine the reason for their presence, a process which knocks them out for several hours. When they awaken they find that they've been taken to the house they were heading for. They are greeted by Sancroff, who seems surprised to find that they're not afraid of him, and then hear the sounds of battle in the distance. The bio-assassins have emerged from the wreckage of the ships and are marching upon the house, and the Drudges' defensive weaponry is ineffective.

The Fifth Doctor materializes in the hold of a British merchant ship, seeking the source of time distortion he had detected in the TARDIS. He locates a tear in the fabric of time and space, but before he can investigate further he hears the voice of Commander Vansell, urging him to return to the TARDIS immediately; all of Time is at risk. The Doctor tries to do so, only to find that his key will no longer fit in the lock and that he is apparently unable to attract Tegan and Turlough's attention -- and as he tries to call out to them, he hears a sound like a distant, ethereal voice. He is confronted by a suspicious crew-woman who demands to know what he's doing here, but before she can take him to the captain to explain himself, the ship is struck by a blast from a German U-boat's deck guns. The woman tries to take the Doctor to the lifeboats, but he insists upon remaining and trying to get back into the TARDIS, and they are thus both still on board when the ship is struck by a torpedo and sunk.

Although sworn to do his duty, Captain Schwieger had ensured that all of the British lifeboats were clear before finishing off the British ship. Lieutenant Zentner spots the Doctor and the crew-woman, clinging to a crate and too far away to reach the departing lifeboats, and Schwieger has them taken aboard, intending to put them off as soon as he can safely do so. British destroyers arrive in response to the merchantman's distress call, and the U-boat departs, separating the Doctor from the TARDIS. Schwieger is suspicious of the Doctor, who is apparently an educated young man who speaks textbook German yet isn't serving in the war and refuses to give his name. The British crew-woman, Helen, suspects that the Doctor is a German spy, and he decides to pretend that he is, hoping to convince Schwieger to turn back so he can get to the TARDIS and leave as the Time Lords had ordered. He claims that he was transporting documents about potential American involvement in the war, and that retrieving the distinctive blue crate containing them is vital to the war effort. Schwieger, however, refuses to turn back and risk his crew without proof of the Doctor's claims, and the Doctor eventually concedes, realizing that Schwieger is only doing his duty.

The Doctor is returned to his cell, but he senses time distortion closing in around him, and when he arrives the rating who was escorting him suddenly goes berserk and attempts to beat him to death for no apparent reason. As they struggle, the Doctor hears the voice of Vansell ordering his execution. Their struggle and Helen's cries for help draw the guards' attention, and Schmidt is taken away under restraint by his horrified fellow officers. The Doctor realizes that the Time Lords were controlling Schmidt, but doesn't understand why they're trying to kill him when he's only trying to return to the TARDIS as they ordered. He doesn't realize that the situation has changed now that he's aboard the U-boat; it is now vital that he be stopped, and despite the Lord President's objections, Vansell diverts all available power to the thought projection link in order to force Schmidt to complete his task.

As Schwieger ponders Schmidt's apparent breakdown and the Doctor's odd trustworthiness, the lookout spots smoke on the horizon from a four-funnel vessel -- it could be the Aquitania, the Lusitania or the Mauritania, and it's heading straight for them, making an easy, tempting target. Meanwhile, Helen tends to the Doctor, apparently accepting his claim that it's vital he return to his TARDIS. Schmidt recovers to find himself strapped down in his cabin, but as he tries to free himself, he hears Vansell's voice echoing in his head again. Once free, he heads for the prisoners' quarters with a gun, and in the ensuing struggle, the Doctor is shot in the shoulder. Schwieger, hearing the shot, abandons his preparations to sink the British ship and takes his officers to investigate. Helen manages to get the gun away from Schmidt and kills him before the Doctor can stop her. Schwieger and his men then arrive, and although Schwieger doesn't believe the Doctor capable of murder, one look at Helen convinces him that she's capable of anything. He has no choice but to return them to the site where he found them.

While trying to locate the third historical distortion, Vansell finds traces of another, female being inhabiting the Vortex at each nexus point. He manages to trace the Sixth Doctor to the Kurgon system, but before he can act, the transduction barrier is breached and alien time ships materialize on Gallifrey. The Knights of Velyshaa demand the unconditional surrender of the Time Lords, and nothing can be done to stop them...

The Sixth Doctor is expelled from the TARDIS following a collision with a temporal anomaly, and recovers to find himself aboard a nearby starliner in the hospitality suite. A waitress named Ellie enters the suite and is surprised to find him there, but she soon recovers herself, concluding that he is one of the delegates. He dismisses the odd feeling that he's met her before and follows her to the conference room, where he learns that he's aboard the starship Edifice with delegates from the Galactic Wonders Commission. They have been invited to study the so-called Kurgon Wonder at close range, but as the Doctor does so he begins to believe that it's far more than a mere "gaseous anomaly"...

In order to give the delegates a close look at the Wonder, the Edifice's android pilot, Azimendah, brings the ship closer to the Wonder than anyone has ever been before -- but an enormous particle disruption field then envelops the ship. As the field sweeps through the conference room, the Doctor recognizes it as a shard of time distortion, and seems to hear a deep voice begging for help. When the distortion passes, the Doctor finds that he and Ellie are apparently the only survivors; everyone else in the room has turned to dust and the ship has aged dramatically. As they set off to search for other survivors, Ellie explains that the Kurgon government was trying to convince the delegates to enter the Wonder into the galactic tourist guide, hoping to boost the planet's economy and end its recession. The Doctor, however, suspects that Ellie is more than she seems; even though she claims not to understand how she survived the time distortion, there remains the question of why she was entering the hospitality suite with a computer disc when she wasn't expecting any delegates to be there. In any case, the Doctor believes the Kurgon Wonder to be a temporal anomaly, and that his TARDIS is trapped inside, along with something else -- something in torment.

Azimendah recovers to find that the ship's systems are barely functioning and that his internal chronometer is apparently malfunctioning. He sets off to search for survivors, and rescues the Doctor and Ellie from a cluster of hideous creatures which are later revealed to be super-evolved bacteria. It appears that they are the only three survivors, out of a passenger and crew complement of over five and a half thousand. As the Doctor explains to the disbelieving Azimendah that he's run into a wave of time distortion from the echo of an ancient temporal explosion, another wave breaches the aging hull. They are forced to flee to the nearest emergency bulkhead, where they find that the controls have aged to dust, but the Doctor recognizes its construction and instructs Azimendah to shoot out the weak points, sealing the bulkhead. The problem is only temporarily solved, however; since the engines cut out while Azimendah was moving the ship into a closer orbit, the Edifice is continuing to drift towards the Kurgon Wonder, and will soon be completely enveloped in the time distortion.

Gallifrey has by now been completely overrun by the Knights of Velyshaa. Despite the low power, Vansell realizes that the time distortion in Kurgon system may enable him to access the positronic brain of the android accompanying the Sixth Doctor. Vansell manages to send one last desperate message before the Knights burst in and kill him and the President. The Doctor must not free the Temperon...

While Azimendah repairs the computer link between the bridge and the engine room, the Doctor questions Ellie further. He is a Time Lord and Azimendah is an android with an extended life span, but there seems to be no reason why Ellie has survived her exposure to the time distortion. She can't explain this, but when pressed about the computer disc she admits that she's part of an underground movement of telepaths who have heard cries of pain from the Wonder. They believe the Wonder to be an ancient catastrophe frozen in Time, but the government, desperate to attract tourism dollars, has tried to silence them. The telepaths were recently able to translate part of an audio transmission recorded in an ancient artefact, which the Doctor realizes is a flight recorder cast out of the explosion at the moment of catastrophe; apparently it contains proof of the telepaths' claims, and Ellie intended to play it back for the delegates. Azimendah returns and catches them with the disc, but the Doctor convinces him to listen, and plays back the recording. It seems that an attempt was made to capture the Temperon, a legendary time beast, but that the Temperon itself tried to destroy the experiment -- resulting in a catastrophic release of temperon particles which suspended it in eternal torment at the moment of its death.

The Sixth Doctor is completely absorbed by the Temperon, but it appears to be in torment, and before it can elaborate upon its warning the Doctor finds himself transported to the Panopticon on Gallifrey -- along with his Fifth and Seventh selves, also brought to Gallifrey by the Temperon. The Panopticon lies in ruins, and the Doctors can sense horror buried in the stone, remnants of the telepathic impressions of terrified Time Lords. But where are the Time Lords, what has happened to Gallifrey, why has the Temperon crossed the Doctor's timestream to bring all three of them together, and who are the Sirens of Time? The Doctors link minds and share their experiences, and realize that the woman accompanying them in each nexus, whether Elenya, Helen, or Ellie, was the same woman each time. She is obviously not what she appears to be, and her manipulations have somehow led to the destruction of Gallifrey.

The Doctors hide from a materializing time ship which the Sixth Doctor recognizes -- it has the same design as the ship formerly frozen in the Kurgon Wonder. The battle-suited occupant, Knight Commander Lyena -- garrison commander of Gallifrey -- is greeted by Sub-Commander Solanec in the name of Sancroff, the leader of the Second Empire of the Knights of Velyshaa. As she berates Solanec for nearly allowing the Temperon to escape, Solanec detects the presence of three Time Lords in the vicinity, and the Doctors flee, pursued by the Knights. They escape by leaping down a service duct, but the Fifth Doctor damages his leg in the fall and the Sixth and Seventh are forced to leave him behind. He is captured and taken to Lyena, who has by now determined who he and his companions are. She heals the Doctor's leg, and reveals, to his horror, what has been done to the rest of the Time Lords...

The Sixth and Seventh Doctors attempt to telepathically track down the Temperon, and while searching for it they stumble across a room full of battle-suits and what appear to be shower cubicles. Sub-Commander Solanec enters the room, but appears to be too weak and disoriented to notice them hiding -- and when he removes his battlesuit they see a wasted, diseased body, the flesh rotting off the bone. Solanec steps into a cubicle for revitalisation, and the Doctors escape and set off in search of the Temperon again. They manage to locate it, and find that it is being kept under restraint while the Knights tap the temperon particles from its body to power the vortex drives of their time ships. Before they can do anything, they are captured and taken to Lyena, who reveals that the Knights are dying -- and that in order to sustain themselves they have captured the Time Lords and placed them in life-extraction units.

The Doctors are outraged, but Lyena informs them that it is their interference which has made this possible. The Seventh Doctor managed to repel the bio-assassins sent to prevent the illegal execution of Sancroff, and the Knights of Velyshaa were thus able to locate and rescue him to lead their second campaign of conquest. The Fifth Doctor's attempt to return to the TARDIS forced the U-20 off course and prevented Schwieger from sinking the Lusitania; although the course of the First World War remained largely unchanged, a petty criminal who otherwise would have died on the Lusitania went on to murder Alexander Fleming in a botched robbery attempt before the discovery of penicillin. The Earth was thus ravaged by new strains of pneumonia and meningitis in 1956, and the survivors never discovered space travel and never defeated the Second Velyshaan Empire. And the Sixth Doctor, by freeing the Temperon, also freed the Knights who had been trapped with it, enabling them to complete their experiment, acquire the power of time travel and thus conquer Gallifrey.

Lyena, however, now reveals that exposure to temperon particles has introduced a mutation into the Knights' gene pool; they are all dying slowly, and although their theft of the Time Lords' lives has slowed their degeneration, soon the life of the Time Lords will be exhausted and the Knights will die as well. There is a single functioning Type 70 TARDIS remaining on Gallifrey, and Lyena wants the Doctors to use it to correct their mistakes; the Knights will thus go out in a blaze of glory after the collapse of their first Empire, rather than being condemned to this slow, dishonourable, creeping death. The Doctors agree to fix their mistakes, although the Fifth Doctor feels that there's still more going on than they know; they still don't know who the woman was in each time zone, why they were sealed out of the TARDIS, or who or what the Sirens of Time are...

Lyena gets the Doctors to the Type 70, but they find that its time core has burned out. They decide to use the Temperon instead, and while the Sixth and Seventh Doctors go to the Temperon chamber, the Fifth Doctor reports the change of plans to Lyena. For some reason, however, this throws her into a panic, and she forces the Fifth Doctor into a life-extraction unit and sends the Knights to stop the other two. They arrive too late, however; the Sixth and Seventh Doctors are making progress, and as the restraint field begins to fail, the Temperon warns them to beware Lyena. The Sixth Doctor fuses the door mechanism to keep out the Knights, and the Temperon reveals that in whatever guise -- Elenya, Helen, Ellie, or Lyena -- the woman they have seen is a manifestation of the Sirens of Time, creatures which feed upon the energy released by distortions in the space-time continuum. It is the Sirens who sealed the Doctors out of their TARDIS and manipulated them into changing history, releasing energy upon which to feed, and creating the Second Empire of the Knights of Velyshaa -- whose destructive use of time travel technology has provided them with even more energy...

Lyena threatens to kill the Fifth Doctor if the others don't surrender, but they refuse and challenge Lyena, forcing the Sirens to reveal their true nature. But the Sirens know the Doctor's true nature as well, and know that he must intervene to set history back on its correct path. The Temperon, however, warns them that each of them has answered the Sirens' call only once; if they obey a second time, they will become enslaved to the Sirens forever, and will be forced to create further distortions in the space-time continuum, providing food for the Sirens until the Universe collapses in a maelstrom of chaos. But if they don't surrender, Lyena will kill the Fifth Doctor, preventing the Sixth and Seventh from ever having existed and releasing more energy for the Sirens. Their only hope is to release the Temperon -- but it cannot destroy the Sirens, merely contain them at the cost of eternal struggle within itself. Lyena is convinced that the Doctor's compassion will force him to act, but the Sixth Doctor points out that in each of his incarnations the basic tenets of his personality balance out differently -- and his sixth incarnation is more pragmatic than his others. He thus destroys the restraint field machinery, setting the Temperon free.