Bev Tarrant and her salvage team have come to the rain forests of Kar-Charrat, to dig up an alien ziggurat which Bev feels sure will make them all rich. Her partner Rappell isn't so sure that this job will be the easy money that Tarrant claims; it's hot, it's pouring rain, and something about the ziggurat makes him profoundly uneasy. It's supposed to be 1270 years old, but there is no vegetation growing on it, and it doesn't feel as though it's made of stone at all. Tarrant dismisses his concerns, telling him that he's been listening to too many stories about the phantoms of Kar-Charrat -- and unaware that her team is being observed by something. Something lurking in a hideout filled with the characteristic heartbeat sound of Dalek technology...

While trying to make sense of the TARDIS library, Ace happens across some particularly old and musty books which the Doctor borrowed from the library of Kar-Charrat long ago and forgot to return. Appalled, he sets off at once, telling Ace that the library on Kar-Charrat holds every scrap of information from every civilised planet in the Universe; it is one of the wonders of the Universe, and the Time Lords helped to install its defence grid, knowing that such knowledge could be terribly dangerous in the wrong hands. To Ace's disgust, the TARDIS materialises in the middle of a jungle, and the Doctor leads her through the pouring rain past a waterfall to what appear to be a set of ancient ruins. As Ace pokes around by herself, looking for something of interest, she hears an odd, wet bubbling sound -- almost like whispers in the rain. The Doctor seems to have vanished, but he steps out of nowhere before her eyes, and leads her through the temporal barrier -- to reveal the Kar-Charrat library in all its glory. Dismissing the sounds in the rain as her imagination, Ace accompanies the Doctor as he explains that the Time Lords hid the library behind a temporal projection of how it will appear thousands of years in the future. Only a time-sensitive can penetrate the barrier without the proper key, and since the library appears to have been destroyed centuries ago, nobody else knows that it is here.

Elsewhere, the TARDIS' arrival has been detected, and the appropriate action is being taken. As Tarrant and her team prepare to unearth the ziggurat, it opens up by itself and something violent emerges -- something which guns down her team without mercy and sets off into the jungle in search of its primary target. But the target has been lost, and it therefore retreats into the jungle to wait for contact to be re-established. Tarrant slowly recovers from the shock of the attack, and her damaged service droid, detecting that Tarrant's leg is seriously injured, uses the last of its power to open its medical pouch before shutting down. Knowing that she's managed to get her friends killed leading them to what she thought would be easy money, Tarrant crawls off through the jungle, trying to get back to her ship. As she goes, she fails to hear the sounds behind her -- sounds like whispers, bubbling through the rainforest. Rappell is dead, and no longer needs his body. But others do...

The library lobby is larger than St Paul's Cathedral, and it's here that the Doctor and Ace are greeted by Chief Librarian Elgin and Cataloguer Prink. Elgin, an effusive and rather pompous old friend of the Doctor's, is delighted to see the Doctor again and looks forward to showing him about the library. It is all but empty now; the staff reside on the upper levels, dealing with agents for new data or passing time in the recreation lounges. The rather embarrassed Doctor returns his overdue books, and the scandalised Elgin blames Prink for not noticing their absence earlier and orders him to return them to their proper place. Ace, taken aback by the emptiness of the facility, asks Elgin whether anybody ever uses it, and Elgin is shocked and scandalised by the thought. If people were actually to read the books here, they would be damaged! Ace, irritated by his attitude, decides to go back to the TARDIS, and Elgin gives her a DNA tag so that she can get past the barriers when she wishes to return. The Doctor quietly tells Ace that although Elgin may be pompous he means well, and arranges to meet her on the second floor reading room later.

As Ace departs, Elgin leads the Doctor to the greatest achievement of the library. At first glance it appears to be a huge chamber full of water tanks, but the Doctor recognises it as an aqueous data storage system -- a "wetworks" facility. This is the largest of its kind he has ever seen, and Elgin proudly claims that it houses the entire knowledge of the Universe. Fascinated, the Doctor bombards Elgin with technical questions, none of which Elgin can answer; all he knows is that it works. He shows the Doctor the retrieval unit, a simple chair and headset which enables the user to download any information into their brain almost instantly. Elgin mentions in passing that a number of races have inquired about the facility, and that some became quite aggressive about demanding access to it. This concerns the Doctor; knowledge can be dangerous in the wrong hands, and this much knowledge in one place makes the wetworks facility potentially the most dangerous weapon ever created. Elgin, however, assures him that the defences installed by the Time Lords are impenetrable. Only one race has ever seriously worried the security staff. A race of robotic creatures called the Daleks...

Elgin is convinced of the reliability of the Time Lords' defences, and doesn't understand why the Doctor is so concerned that the Daleks know of the facility's presence. They did try to attack the library once, but failed to blast their way through the barrier and gave up. When Elgin admits that the attack was not really a full assault -- it was more like a test, as if the Daleks were trying to prove to themselves that they couldn't get in -- the Doctor becomes even more concerned. It's not like the Daleks to give up, and it may not be safe for Ace to wander around outside. Elgin reluctantly accompanies the Doctor out beyond the barrier, where he is shocked to find Ace and Tarrant lying unconscious in the ruins. The Doctor has them both taken back into the library's medical facility, where Ace recovers and claims that they were both attacked by an animal which lunged out of the forest before she could get a look at it. There's something a bit off about her responses, and the Doctor, concerned that she may be suffering from delayed shock, tells her to rest in the medical bay for a while. He and Elgin depart, leaving Ace alone with the unconscious Tarrant. Or at least they would be doing so, if this were the real Ace...

Ace is a prisoner of Dalek Scout Seven, the special weapons unit which killed Tarrant's crew and hunted Ace to the library ruins. It has reported its success to a Dalek mothership which is now entering geostationary orbit and preparing to engage in battle. To Ace's shock, the Daleks reveal that they intended to capture her all along; she has been duplicated and her DNA tag has been given to her clone, who will penetrate the temporal barrier and shut down the defence grid, granting the Daleks access to the library at last. Ace is to be kept prisoner on the mothership, in case the duplicate requires access to her brain patterns to remain undetected. While Scout Seven reports on surface conditions and the battle computers are updated, Ace learns that the Daleks have used time corridor technology to plant agents on every planet in the sector, and have waited hundreds of years for a Time Lord to arrive. And now the Doctor has finally returned, and the Daleks' capture of the Kar-Charrat facility is inevitable.

The Doctor wonders why Tarrant is here, given that the library is supposed to be a secret. Elgin suggests that she's here to study the ziggurat, supposed to be the relic of an ancient civilisation. The Doctor, curious, sets off to examine the ziggurat himself, accompanied by the weary Elgin -- whose weariness gives way to shock when they find the bodies of Tarrant's crewmates lying in the jungle near the ziggurat. It appears obvious from their equipment that they were here to steal the ziggurat and sell it to a collector, but what's more interesting is the amount of human blood on the ground. There's more here than could have come out of Tarrant, but there is no human body nearby. The Doctor wonders whether something other than the Daleks is at work here, and recalls Ace's comment that she heard something in the ruins earlier. The last time he was here, he also recalls hearing tales about ghosts in the jungle, stories which Elgin dismisses as foolish spaceport rumours. Putting aside this mystery for the moment, the Doctor and Elgin continue on to the ziggurat, which to Elgin's horror has been opened from the inside. As the Doctor feared, it is not an ancient artefact at all, but a Dalek deep hibernation unit -- with activation sensors rigged to wake the hibernating Dalek when they detect the arrival of a TARDIS nearby. Elgin spots a cloning chamber in the corner, and the Doctor finally realises, to his horror, just why Ace was behaving so strangely in the medical bay. The Daleks weren't after him at all, but his companion -- and he has just left a Dalek duplicate alone in the library, with access to the defence grid!

The Daleks impatiently await word from Ace's duplicate. The test subjects have been prepared for data acquisition, and the scientific division is poised to access the wetworks facility and begin downloading. Ace-2 reaches the defence grid, activates her voice synthesiser and uses Elgin's voice to bypass the security protocols and shut down the barrier. The Dalek mothership detects fluctuations in the defence grid, and the Dalek Supreme orders his troops to attack. Meanwhile, the disoriented Tarrant wakens in the medical bay to the sound of alarms as the library's defences shut down -- but amongst the confusion she hears a bubbling sound like a whisper of her name. And her dead partner Rappell steps out of the shadows, begging her for help.

The Doctor and Elgin have no choice but to try to return to the Doctor's TARDIS and send out an SOS to the Time Lords. Dalek patrols have been sent out into the jungle to look for them, and they are forced to take a roundabout route to avoid detection. As they do so, the whispering, bubbling sounds become ever more urgent. There's definitely something else out here in the jungle with them. Something upset...

The Daleks exterminate all unnecessary life forms in the library -- in other words, everybody -- and prepare to link the first test subject to the wetworks facility. The Dalek Supreme reports the progress of the operation to the Emperor on Skaro, but admits that the Doctor has not yet been captured. The Chief Scientist predicts a 70 percent possibility of failure if a Time Lord's neural pathways are not used as a buffer to filter the data download, but the Emperor will not tolerate any delays to its invasion plans and orders the Dalek Supreme to attempt the procedure without the Doctor. Tarrant is brought before the Dalek Supreme to explain her presence on the planet, and although the Daleks conclude that she is irrelevant, they decide to keep her alive in case a lure is needed to bring the Doctor out of the jungle. As Ace-2 takes Tarrant away under guard, the wetworks facility is brought on-line, and the first test subject is connected to it; however, when the Daleks try to download the knowledge of the Universe into its memory circuits, it is unable to handle the data flow. The Dalek's memory circuits overload, and it goes mad, breaks out of its restraints and hurtles off into the corridors, screaming in agony and firing at random as its fellow Daleks pursue it. Without the neural buffers of a Time Lord such as the Doctor, the Daleks can only survive the experiment by downloading the data at a slower rate -- which will mean a delay to the invasion. This is unacceptable. The Doctor must be captured immediately!

The Doctor and Elgin find the TARDIS surrounded by Daleks, and the Dalek Supreme arrives and threatens to kill Ace, Tarrant and Prink if the Doctor does not give himself up. The Doctor, aware that these could be duplicates, is unable to take the risk and surrenders to save their lives. He and Elgin are returned to the library with the others, where the Daleks inform them that they intend to create a Dalek with the complete knowledge of the Universe -- a mobile data store with which they can conquer the Universe, one planet at a time. The Doctor, Ace and Tarrant are left under guard by Ace-2 while Elgin and Prink are forced to repair the damage caused by the rogue test subject. The Doctor tells Ace about the noises he heard in the rain, apparent evidence that there is another force at work on the planet -- and the shocked Tarrant realises that her dream of Rappell in the medical bay wasn't a dream after all. It appears that the phantoms of Kar-Charrat are real -- but if so, why do Elgin and the others dismiss them as nothing more than stories?

Elgin and Prink repair the damage to the wetworks facility, and are forced to stand by and watch as the Daleks bring in the Doctor. The sickened Elgin has no choice but to connect the Doctor to the retrieval interface, and the Daleks prepare to download the wetworks' data into a second test subject. This time, the natural neural buffers within the Doctor's Time Lord brain are capable of handling, filtering and compressing the rapid data flow, and the Dalek test subject survives -- and acquires the accumulated knowledge of the entire Universe. But the agony has been too much for the Doctor to bear, and the grief-stricken Elgin discovers that the process has killed him. As the Dalek test subject assimilates the knowledge it has acquired, the Dalek Supreme returns to the mothership to report the success of the operation... and to prepare to destroy the Kar-Charrat facility behind them.

Fortunately, the Dalek is completely unbalanced, and its weaponry is operating outside safety tolerances -- which means that it misses its aim completely and blows a hole in the library wall, through which Ace and Tarrant flee to safety. "Rappell" remains behind to hold off the Dalek, and the horrified Tarrant is forced to watch as her lover is blasted apart for a second time. But when the Dalek pursues them out of the library, the rainfall suddenly seems to concentrate itself over the Dalek -- and it drowns within its own casing. The voice of "Rappell" speaks to Ace and Tarrant, who realise that the sound is coming from the rainfall itself. The Phantoms are the true natives of Kar-Charrat, a living essence which can inhabit any form of water; the rivers and the oceans, the waterfall, the rain, everywhere water is to be found on the planet. Since the human body consists largely of water, Rappell's dead body was able to act as a host for the Phantoms' intelligence as they tried to contact someone who would listen to them -- someone who would understand the crimes the librarians have committed against the Kar-Charratians...

The Doctor finds his mind floating disembodied in the wetworks facility itself, where the Kar-Charratians are finally able to speak with him. They saved him at the moment of his death by uploading his consciousness into the wetworks facility -- where they exist themselves in torment. To the Doctor's horror, the Kar-Charratians reveal that the wetworks unit is not a technological miracle, but a gulag where their species has been enslaved, their minds wiped clean. Each drop of liquid in the wetworks storage tanks is or was a living being, and as the librarians replace the living Kar-Charratian minds with the data from the library, they are wiping out an entire race. The Doctor, infuriated, promises to free the Kar-Charratians -- but they warn him that he will have to act quickly, for the Daleks intend to destroy the entire library when they depart.

The Daleks detect the destruction of the rogue, and the Dalek Supreme orders the test subject to explain. With its new storehouse of knowledge, it understands that the native life forms of the planet are capable of invading Dalek casings and rendering them inoperative -- but to the Dalek Supreme's fury, it insists that the natives are non-hostile, and refuses to advise on the correct procedure for the natives' extermination. The "erratic" behaviour of the test subject suggests that a second may be required, and since the Doctor is dead, this means the Daleks will have to attach the remaining prisoners to the data retrieval unit, burning out their minds one after another until successful transfer is achieved. The Dalek Supreme reports the problem to Skaro, but the impatient Emperor Dalek will brook no further delays. Infuriated that the Dalek Supreme has foolishly killed the Doctor before he could be interrogated, the Emperor orders it to return to Skaro and destroy the facility immediately. The Dalek Supreme has no choice but to obey.

The Daleks leave the dispirited Elgin and Prink locked up in the wetworks facility, and once it's safe, the Kar-Charratians download the Doctor's mind back into his body. Elgin is overjoyed at first, until the furious Doctor accuses him of unspeakable crimes against the Kar-Charratians. He had counted Elgin as a friend, and all along he no better than the Daleks! Subdued, Elgin shows the Doctor the way out, and they manage to avoid the Dalek patrols and slip out of the library through the hole blown in the wall by the rogue Dalek. Their escape is discovered, and the chief scientist examines the remains of the rogue Dalek and determines that it was drowned within its own casing. The Daleks cannot venture out into the jungle to recapture the prisoners. But Ace-2 has no such weakness...

The Doctor, Elgin and Prink are reunited with Ace and Tarrant outside Tarrant's ship, which she doesn't dare power up in case the Daleks detect it. The Doctor takes them back to the TARDIS, planning to blow a hole in the wetworks facility and release the enslaved Kar-Charratians into the rainfall. Elgin claims that he never knew the natives were intelligent, but is forced to admit that he never tried to communicate with them; the library has been his life's work, and he long ago lost the ability to see anything beyond it. The Kar-Charratians kill the Daleks guarding the TARDIS, but before the Doctor can enter Ace-2 arrives and captures Elgin, threatening to kill him if the Doctor does not surrender. Prink finally snaps and attacks Ace-2, rescuing Elgin and shooting the duplicate in the chest. Ace-2 snaps his neck, but the Kar-Charratians flood into the hole in her chest and short out her internal circuitry. Elgin, stunned by Prink's death, offers no resistance as the Doctor prepares to take the TARDIS into the library, to destroy the wetworks facility for good.

The Daleks detect the arrival of the TARDIS and are waiting for the Doctor when he emerges, but Ace pretends to be her duplicate, and claims to have taken the Doctor prisoner and killed his friends. The Dalek Supreme orders his followers to move the TARDIS to the mothership, and to destroy the facility behind them -- but the test subject intervenes, claiming that the destruction of the library and the extermination of the Kar-Charratians serves no logical purpose. Since it has the superior intellect, its orders should be obeyed, not those of the Dalek Supreme's. As the furious Dalek Supreme orders the test subject to obey, Ace manages to plant explosives on the wetworks storage units, and when the Dalek Supreme notices what she is doing, the test subject opens fire upon it, refusing to let it harm Ace. Life must be protected, not exterminated. As the Daleks open fire on the rebellious test subject, the Doctor sets the data retrieval unit to download at the moment the explosives blow, and retreats to the TARDIS with Ace.

The Dalek Supreme retreats to the mothership and flees, and although the test subject is finally destroyed by a Special Weapons Dalek, the remaining Daleks have no time to defuse Ace's explosives. The data storage units trigger a download just as the tanks are smashed open by the explosives, and the Kar-Charratians are freed at last. The remaining Daleks are drowned within their casings by the vengeful Kar-Charratians. The Dalek Supreme is forced to retreat, and to report failure to the Emperor Dalek. The infuriated Emperor orders it to place the Chief Scientist in command and to self-destruct, which it does. This is only a setback, the Emperor insists; an alternate plan will be devised and the Dalek invasion will succeed. Nothing will stop them!