Somewhere in the shadows on Gallifrey, a Time Lord conspires with a creature from the Universe of anti-matter, intending to use the Doctor as the subject of their transfer. The traitor transmits the Doctor's bio-data extract from the Matrix, but the transmission is detected by two technicians, Damon and Talor. Talor attempts to report the security breach, but cannot reach the Castellan -- and later that night, Talor is murdered by the traitor, who destroys the communications console to erase the evidence of his crime and make Talor's death appear accidental. He reports the incident to his ally and advises caution, but it is too late. The Doctor's TARDIS is already coming under the Creature's control...

The Doctor has repaired the audio circuits on the TARDIS scanner, which might impress Nyssa more if there were anything to listen to outside. As she begins to remind him of the other systems that need repair, including the navigational system and the temporal grace circuits, the TARDIS goes out of control, converging with a massive source of magnetic radiation. Unable to change course, the Doctor and Nyssa flee the console room when they see a point of light curving through space towards them. Time slows down as the energy breaches the TARDIS' interior dimensions, transforms into a fountain of light and envelops the Doctor. For a moment, his body is overlaid by an image of the Creature, which then vanishes. As the Doctor recovers, he tells Nyssa that something from another Universe has linked itself to his biology, gaining a foothold in this dimension -- and when Nyssa checks the TARDIS console, she discovers that the Creature is made of anti-matter. If the link fails, the results could be catastrophic...

Two young hikers, Robin Stuart and his Australian friend Colin Frazer, have arrived in Amsterdam earlier than expected. Colin's cousin isn't due in until tomorrow, and all of the youth hostels are full; therefore Robin, who recently lost his passport and doesn't want to attract attention, leads his friend to Frankendael, a neglected mansion owned by the state. He intends to spend the night next to the crypt, in one of the pumping stations which keeps Amsterdam above water. Colin isn't pleased by the thought of sleeping in a crypt and spends the night fully dressed and not entirely asleep. Thus he is the one to hear a strange vworping sound and see a flashing light in the crypt later that night. Unable to wake Robin, he investigates alone -- and is shot and apparently disintegrated by a monstrous figure which stalks out of a tomb that wasn't there before...

The Doctor and Nyssa analyse their encounter, and discover that things are worse than they feared. This area is the Arc of Infinity, an ancient curve between the dimensions, and it appears that the Creature can control its shift. It is also the location of a collapsed Q-star, and is thus awash with quad radiation, which has the property of being able to shield anti-matter. Temporarily. In order to exist in this Universe permanently, the Creature must make a full bond to the Doctor's genetic print, and for it to get as far as it already has, someone on Gallifrey must have transmitted full details of the Doctor's biodata to it. The Doctor and Nyssa must track down the Creature before it reverts to anti-matter, but it could be anywhere in the Universe... and then the matter is taken out of their hands in any case. The Time Lords have detected the incursion, and have no choice but to act at once. To Damon's surprise, Commander Maxil of the Chancellory Guard arrives in Time Control with an order issued directly from the High Council. The Doctor's TARDIS is to be recalled to Gallifrey immediately, and transducted to the security compound in the heart of the Citadel...

Robin awakens, realises that Colin is missing, and investigates, only to be attacked by the monster in the crypt. He bolts in terror, and after quaking on the cold streets for some time he returns for his belongings -- to see the walking-dead Colin installing alien machinery in the pumping station. Terrified, Robin flees, and reports Colin's "disappearance" to the police; however, he is unable to give any details about his insane experience and thus cannot interest them. Dispirited, Robin goes to the hostel where he and Colin had booked rooms, to find a message waiting; Colin's cousin will be arriving at the airport tomorrow...

The guards drag the stunned Doctor back to the TARDIS, where Maxil removes the ship's space-time element and orders his guards to use lethal force if the Doctor tries to escape again. While the Doctor recovers, the Castellan reports the incident to President Borusa, and as soon as all is prepared, the Doctor and Nyssa are brought before the High Council. Only the Doctor's old friend Hedin seems pleased to see him; Cardinal Zorac is distressed by the violence which has once again accompanied the Doctor's return, while Chancellor Thalia pointedly reminds the Doctor that he has disobeyed their orders to return to Gallifrey before. The Doctor in turn reminds Thalia that Romana chose to remain in E-Space of her own accord.

President Borusa arrives and the High Council formally convenes, but the Doctor soon realises they have dismissed out of hand the idea that one of them could be a traitor. As the Creature has already breached the Matrix, the matter is now critical -- and the decision has already been made. The Doctor is to be confined until a Warrant of Termination can be issued, at which point he will be taken to a place of execution... and the Creature's link with this Universe will be severed. As Maxil and his guards drag the protesting Doctor away, Nyssa desperately pleads his case, but to no avail. If the Time Lords allow the Doctor to live, they condemn untold millions of innocents to death when the Creature reverts to anti-matter. Again, her allegations that one of the Council must be a traitor are dismissed by all; however, as she storms out of the Council chambers, the concerned Hedin privately asks the Castellan if he intends to investigate these claims. The Castellan refuses, claiming that he would be sure to know if such a serious security breach had occurred. Everything is going just as the traitor and the Creature had planned...

Colin Frazer's cousin arrives at Schipol Airport, and Robin is faced with the difficult task of explaining what has happened. Fortunately for him, Colin's cousin is the Doctor's former companion Tegan Jovanka, and she is less sceptical than Robin might have expected. Robin can't press the police to take action, due to his lost passport, and when Tegan tries going to the police herself she gets no further than Robin had. It seems that it's up to them to rescue Colin themselves, and Robin thus reluctantly leads Tegan back to Frankendael and whatever is lurking in the crypt...

Damon manages to contact the Doctor as he is marched back to the security compound, and slips him a print-out of the security traffic proving that his bio-data extract was indeed transmitted from Gallifrey. Damon then contacts Nyssa and explains his situation to her; although he knows that one of the Council is a traitor, he doesn't know which one, and thus can't approach any of them -- particularly not after Talor's "accident". They ask Hedin for permission to visit the Doctor before his execution, and Hedin arranges a visit through the Castellan, who intends to eavesdrop on their conversation; however, his plan fails when Damon tells Maxil that they have permission to speak privately. The Doctor ushers Damon and Nyssa to Nyssa's room before Maxil can protest, and once they're out of earshot they discuss Damon's revelations. The Creature might very well be able to seize control of the Matrix if they can't stop it. The Doctor orders Damon to find out if any power equipment has been transported off-world recently, and to fit the TARDIS with a new space-time element -- preferably one without a recall circuit. Before he can say anything else, Maxil arrives -- and to Nyssa's surprise, the Doctor simply tells her that he will not be filing an appeal.

The grief-stricken Nyssa flees back to the TARDIS, where Damon learns that his repairs have been to no avail. Meanwhile, President Borusa confirms that all trace of the Creature has been expunged from the Matrix. Or so it appears. In fact, the Creature is still very much in control -- and the Doctor is alive, his mind suspended in the Matrix while his body remains hidden behind a force shield in the termination cubicle. The Doctor had gambled on the Creature having prepared for his execution. He now demands to know its true identity, guessing that it refused to contact the Time Lords directly because it is already known to them. The Creature claims only that it wishes to return to the Universe which it once inhabited, but the Doctor refuses to let it seize control fo the Matrix in the process. The Creature thus abandons him to his thoughts until he's ready to listen.

Tegan and Robin return to the pumping station, to find that the door to the crypt is locked -- but Colin's rucksack and sleeping bag remain. They hear someone approaching, and hide as the hypnotised Colin enters the room and begins to operate the alien machinery connected to the pumping station. He then returns to the crypt, and Tegan shakes Robin off and follows -- only to be shot and disintegrated by the monstrous Ergon, as is Robin when he follows her...

The Castellan, disturbed by the strange incident during termination, orders Maxil to investigate discreetly. Maxil soon discovers that the termination circuits were rigged to cut out at the moment of execution -- and in the process, he finds proof that the Doctor's bio-data extract was indeed passed on from Gallifrey. The Castellan has Damon and Nyssa brought to him for interrogation, and is unimpressed when Damon admits that he suspected the Castellan himself of treason. The Castellan, believing that the Doctor is conspiring with the Creature and the traitor to seize control of the Matrix, orders Damon to run a full analysis of the rigged termination, and then sets off to inform the High Council of his discoveries, leaving Nyssa and Damon locked in the control room.

Tegan and Robin awaken to find that they have been reconstituted inside a TARDIS. The Creature has its Ergon scan their minds for possible use, and learns, to its surprise, that Tegan is known to the Doctor. Its ally then warns it that the Castellan is on their trail. Time is of the essence, and the Creature must concentrate all of its energy on transfer -- which means that it must release the Doctor. The Creature thus contacts the Doctor and reveals that Tegan is its prisoner; should the Doctor try to take advantage of his freedom to act against the Creature, she will die. The Doctor gives his word, and the Creature releases him -- and then, to show its gratitude for Tegan's service, it releases Colin's mind from its thrall, reuniting the dazed and drained Colin with his cousin.

The Doctor reaches the control room without being spotted, and is reunited with Damon and Nyssa. He now knows that, to have taken Tegan prisoner, the Creature must be on Earth, but he needs a more specific location. Damon reports that a fusion booster, an experimental piece of equipment capable of converting vast amounts of power from anything containing hydrogen, was recently transported to Earth -- and that the Presidential codes were used to authorise the transport. Meanwhile, the Castellan reports to the High Council that the Presidential codes were used to transmit the Doctor's bio-data extract and to save him from termination. The Castellan believes that Borusa, the Doctor and the Creature are conspiring to relocate the shift of the Arc of Infinity to Gallifrey and link it to the Matrix, thus releasing a vast amount of power which only those who have already communed with the Matrix will be able to control.

Omega cuts off communication with the Time Lords, furious that Hedin has been killed. Realising that Tegan is his only hope of locating Omega, the Doctor sends Nyssa back to the TARDIS and connects himself to the Matrix to speak with Omega directly. He claims to have given up fighting Omega, and asks to speak to Tegan so he will know she remains unharmed. Tegan risks her life to give the Doctor clues to her location -- Amsterdam, a crypt behind a fountain, and the initials "JHC" -- before the angry Omega expels her from the Matrix again. The Doctor joins Nyssa in the TARDIS, while the Councillors join Damon in the control room and fire a pulse loop into the Matrix to distract Omega. The Doctor manages to leave Gallifrey unnoticed before Omega tracks down and disables the pulse. All the Time Lords can do now is wait and hope he will succeed... but the Castellan, at least, has learned not to underestimate him.

The Doctor builds a breaker to short out Omega's fusion booster and feed the energy back into his transfer equipment. The TARDIS arrives in Amsterdam, and a quick perusal of the phone book reveals that JHC is an acronym for youth hostels. Unfortunately, as neither the Doctor nor Nyssa have Dutch coins for the telephone, they must check each hostel on foot -- and with every minute the concentration of anti-matter in the vicinity increases. Finally, the receptionist at one particular hostel recalls an Australian on the register, and his fellow receptionist -- who spoke with Robin upon his arrival -- recognises Tegan's name and gives the Doctor a message Robin left in case he missed her at the airport.

Robin's message directs the Doctor and Nyssa to Frankendael, where they find the fountain, the crypt, the pumping station and the fusion booster which Omega is using to shift the Arc of Infinity to Amsterdam. The Ergon detects the Doctor tampering with the booster and attacks him, but the Doctor fights it off and Nyssa shoots it with its own matter-converter gun. Identifying the Ergon as one of Omega's unsuccessful attempts at psycho-synthesis, the Doctor leads Nyssa to Omega's TARDIS, where Omega is twisting in agony as his body-suit melts in the energy of the transfer. Omega threatens to kill Tegan if the Doctor doesn't back down, but the Doctor's sabotage then takes effect and the energy feeds back into Omega's TARDIS. Omega refuses to give up, however, and he makes the final jump across the Arc moments before the feedback destroys his ship. Standing amidst the ruins of his TARDIS, Omega strips off his face-mask to reveal the features of the Doctor. The Doctor warns him that the transfer is unstable, but Omega ignores him and departs in triumph as the Doctor and Nyssa search for the matter-converter gun -- now their only means of stopping Omega before he reverts to anti-matter.

Outside, Omega kills a gardener and steals his clothing, and heads out into the streets. Back in the world of the living once more, suddenly Omega no longer seems a power-mad megalomaniac, but a wide-eyed child staring at the world in wonder. But as he rests by a canal, he catches sight of his hands -- and sees their skin rotting away. As the Doctor had warned, the transfer is unstable, and Omega flees into the streets in horror as the flesh starts to slough away from his hands and face...

The Doctor locates and repairs the Ergon's gun, and after ensuring that Colin and Robin are all right, Tegan joins him and Nyssa as they pursue Omega from the TARDIS. Omega's condition has deteriorated even further, and although the Doctor and his friends nearly lose him several times, they soon locate him by following the sound of screams. Eventually they corner Omega at the end of a pier. Exhausted, weary, and no longer looking even remotely like the Doctor, Omega realises that all is lost, and deliberately wills the accelerated decay of his shielding. He will not return to the living death of the anti-matter Universe, and if he must die, he will take the Earth with him. The Doctor has no choice but to shoot him with the matter-converter, destroying Omega's disintegrating body before it converts to anti-matter. Back on Gallifrey, the Time Lords detect the Doctor's success, but Borusa feels no triumph -- only pity, and the hope that Omega has found peace at last.