Inquisitor Darkel and Cardinal Braxiatel are presiding over a judicial inquiry to decide whether Romana’s response to the crisis on Gryben were justified. It seems, however, that none of the lesser races have the ability to construct a timonic fusion device of the sort supposedly called into play on Gryben, and the Time Lords no longer have access to the raw materials necessary to construct such a device; therefore, the device on Gryben cannot have been a true timonic fusion bomb, in which case, Romana must have overreacted.

Though supposedly impartial, Braxiatel intends to be “impartial on the wrong side,” and he knows that the Time Lords themselves actually did construct such a device in the past. Braxiatel warned Glower, the Time Lord in charge of the test, that the effects of the explosion would be far more devastating than Glower had predicted, and although Glower initially dismissed his fears, the test was in fact called off at the last moment. Narvin, now the Co-ordinator of the CIA, was the one who actually stopped the countdown, and the timonic fusion device was later dismantled. But only Narvin knows why the test was really called off.

Torvald comes to realise that Narvin has not told him everything about the timonic fusion device, and Narvin admits that the Time Lords did construct such a device once, although it was never used. He accesses the Matrix to show Torvald the evidence, and at the very same time, K9 Mark II accesses the Matrix on Romana’s instructions to find data on Project Alpha. If they can analyse the temporal frequency of the original device, they may be able to trace the current location of the one from Gryben. Narvin and Torvald are forced to disengage before K9 detects their presence in the Matrix, but soon K9 has a much greater problem to worry about. There’s a sealed data store within the Project Alpha data, and when K9 analyses it, he discovers that it’s a data bomb which he’s just triggered. Within 5 microspans, it will detonate, and if the bomb contains a virus, the entire Matrix will be compromised.

Braxiatel advises isolating the data bomb and suspending the Matrix’s real-time regulator for that section, thus delaying the detonation. K9 does so with seconds to spare, but must draw on his own power source to keep the clock stopped; once his reserves have been depleted, the data bomb will detonate. He has successfully calculated the frequency of the original timonic detonation, and with this information, Romana and Braxiatel can locate the second bomb -- but it now occurs to Braxiatel to wonder where this data came from if Project Alpha was never actually detonated in the first place. Braxiatel had flattered himself that Glower finally listened to his pleas and gave in -- but what if the Time Lords did go ahead and test the device in secret?

Meanwhile, Leela has concerns of her own. Having learned that the Matrix collects information on everything that happens in the Capitol, she wants to know if it knows what happend to her missing husband, Andred. Braxiatel apologetically informs her that the Matrix may have considered this information of low priority and thus forgotten it.

The inquiry resumes, and Romana presents Darkel with new evidence proving that the timonic device from Gryben was not removed from Gryben at all, but transported one day forward in Time. Narvin suggests sending a CIA team to recover it, and scoffs when Braxiatel suggests that the Chancellory Guard be sent instead -- and Leela notes that Narvin, when sniping at the Guard, refers to Andred as her “late” husband. Romana and Narvin reach a compromise: Torvald will take in a CIA team to recover the device, but Leela and K9 Mark I will accompany them as impartial observers.

As Narvin briefs Torvald on his mission, Leela and K9-I eavesdrop on their conversation, and learn that Narvin has found a way to identify who planted the data bomb in the Matrix by analysing his or her artron imprint. He seems to suspect Romana herself, and Leela thus passes on a warning to Braxiatel before leaving. Braxiatel in turn advises Leela to check out Andred’s biodata extract in the Panopticon archives to see if she can learn anything more about his disappearance. Leela and K9-I then accompany Torvald’s team to Gryben, where they find a group of android servitors, the consignment which went missing from the temporal summit, preparing to collect the timonic fusion device. Leela joins in the battle, but, perhaps due to the CIA team’s incompetence, the servitors manage to self-destruct before any can be captured and analysed; thus, though the CIA team recovers the device itself, they have no way of knowing who sent the servitors to collect it.

Back on Gallifrey, K9 Mark II continues to hold the data bomb in check, but his power will soon be exhausted. Braxiatel leaves to deal with other business, noting gloomily that if he had planted the bomb, he’d have left no way to prevent its detonation. Leela reports to Romana, and suggests that Torvald may have deliberately allowed the servitors to self-destruct so they could not be analysed. Also, before the attack he told her to “try not to kill anyone,” in almost exactly the same tone of voice Andred used to use. Leela is now convinced that Torvald knows more about her husband’s disappearance than he’s saying, which implies that Narvin himself must be involved.

Meanwhile, Narvin has traced the artron imprint of the data bomb and has found evidence that the Time Lord responsible has been travelling in the outer Universe. The traces do not match Romana’s known movements -- but Torvald finds a bill of sale with the guilty Time Lord’s name on it. After some further investigation, Narvin contacts Romana, demanding to speak with her privately. Romana orders K9 not to listen, and he diverts power from his sensors to the circuits holding the data bomb in check. Narvin then reveals the identity of the guilty party, and provides Romana with incontrovertible evidence that the Time Lord in question has been out in the Universe, buying up artwork, sculpture, furniture, and even whole buildings. Shocked, Romana decides to visit the most relatively recent transaction to confront the guilty party, and although Narvin objects to her leaving Gallifrey in the midst of this crisis, she refuses to take action against the accused before seeing the truth for herself.

Romana has advised Leela to leave Narvin alone, but Leela visits the Matrix archives with K9-I -- ostensibly to look for data on Project Alpha, but in fact to look up Andred’s biodata extract. The archivist helps her to locate it, but is surprised to find that the slot is empty -- and the last person to access the data is classified, implying that it must have been a high-ranking CIA official with the authorisation to remain anonymous. Torvald’s extract was retrieved at the same time, and when Leela reaches out for it, she drops it -- and its cap pops off. Strangely, it appears that the colour-coded cap which identifies Torvald as a member of the Arcalian chapter has been deliberately cut off and then replaced. K9 accesses records denied to even the archivist, and reports that the key used to access Andred’s biodata extract belonged to Narvin -- and was last used by Torvald.

Romana visits a museum in the outer Universe where the guilty Time Lord recently arranged to purchase a rare sculpture by the artist Serafina. Posing as an employee of the purchaser, Romana pays for the sculpture and leaves a message with the seller telling the purchaser -- Irving Braxiatel -- to meet her in the ruins of Cholesteron in 12 hours’ time. Braxiatel turns up on schedule, thus confirming that he has broken the laws of Time and interfered in the affairs of other worlds, buying up priceless works of art for his own private collection. Romana had heard of the Braxiatel Collection once before, but never made the connection until now. Braxiatel admits that he began to set up the Collection in order to preserve the artworks of the galaxy after Project Alpha came so close to destroying so much, but when Romana accuses him of planting the data bomb to cover his tracks, he denies doing so. He had considered planting such a bomb, but for different reasons, and when Project Alpha was called off he had no motive to do so. He and Romana now realise the truth -- but there’s only one way to prove it...

From Braxiatel’s perspective, this conversation occurred some time in the past, and he has since returned to Gallifrey -- where Narvin now decides to take action without waiting for Romana to return. Torvald thus arrests Braxiatel on charges of interfering in the affairs of other species. Leela witnesses the arrest and tries to warn Romana, only to find Narvin waiting in her office. Leela takes the opportunity to question him about Andred, and threatens to kill him when he refuses to answer her questions. Realising that she’s not bluffing, Narvin reluctantly admits that Andred came to him some time ago, claiming that he now sympathised with Narvin’s position that Gallifrey must remain aloof and isolated -- because his association with the primitive and savage Leela had convinced him of Gallifreyan superiority. Convinced that Andred was bluffing in order to gain his trust and infiltrate the CIA, Narvin sent Torvald to meet Andred in the lower levels of the old city, but Andred apparently ambushed Torvald and tried to kill him. Andred was killed in the exchange of gunfire, and Torvald was so badly injured that he had to regenerate. Torvald arrives and overpowers the furious Leela, insisting that he acted in self-defence.

Romana returns to Gallifrey to find both Braxiatel and Leela under arrest. Braxiatel has admitted his crimes, but insists that he’s acting for the good of all species in the galaxy; however, Romana dismisses this as a side issue and insists that Braxiatel tell the truth about the data bomb. He admits that he planned to plant such a bomb in the event that Project Alpha had gone ahead -- but since it was called off, why is the data bomb in the Matrix anyway? There’s only one way to find out: they must let the data bomb detonate. Unfortunately, K9-II has just found a way to tap into the Capitol’s power systems, ensuring that he can keep the clock stopped indefinitely, and since he’s shut down his sensors, he can’t perceive Leela or K9-I telling him to let the bomb go off. K9-I thus shoots his counterpart with a low stun blast, disabling him. The Matrix clock resumes countdown, and the data bomb explodes.

The data from the bomb contaminates every part of the Matrix -- but it is not a virus. Rather, it contains the truth about Project Alpha. According to the data from the bomb, the test did go ahead after all -- and, just as Braxiatel had predicted, the explosion was far more powerful than the Time Lords had anticipated, and the shockwave destroyed the planet Minyos before anyone knew what was happening. The High Council launched a cover-up, claiming that Minyos had been destroyed in a civil war. Braxiatel then planted the data bomb as insurance, ensuring that the truth about Project Alpha would be disseminated throughout the Matrix for all to see if the High Council ever tried to assassinate him.

However, this is no longer what actually happened. Narvin is now forced to admit the real reason the test was called off: at literally the last moment, he discovered that someone had stolen the timonic fusion device. The High Council, unwilling to admit that such a powerful weapon had simply gone missing, covered up the entire affair and let Braxiatel think he was responsible. The truth is now apparent: someone travelled back through Time to steal the Time Lords’ timonic fusion device for use on Gryben, changing the Time Lords’ own history in the process; but since the Matrix exists outside relative time, it was unaffected, and the data bomb which Braxiatel originally planted in the Matrix before history was changed remained intact.

History must be set back on its proper course, and since Torvald’s team has already botched one mission, Romana decides to do so personally. She and Braxiatel travel back through Time, and their TARDIS materialises within the transduction barriers protecting the timonic fusion device, and there, they find the hijacked squad of android servitors preparing to steal the bomb. Romana and Braxiatel gun down the servitors and retreat, allowing Project Alpha to continue -- though this means that the detonation of the timonic fusion device destroys the planet Minyos.