12 December 2003. The National Foundation for Scientific Research in Berkshire is holding its centenary celebrations, and Dr John Hallam has invited his niece, a computer expert whom he hasn’t seen for some time. After chatting with John about the ceremony, the institute’s director, Dr David Munro, meets with Rachel, his press secretary, to run through the schedule. Rachel will introduce Munro to the press, he will give a short speech about the Foundation, and then they will go outside for the ceremony itself. Munro is to bury a time capsule in the grounds -- or at least dig out the last spadeful of dirt from the hole, place the capsule within and drop some dirt over it. The preliminary work has already been completed by the Foundation’s grounds staff, who will finish burying the capsule once the press have taken their photographs and returned inside for the champagne reception.

Somehow, the Doctor manages to pick up Mel’s mail, including her uncle’s invitation. Mel looks forward to seeing John again, while the Doctor anticipates seeing old friends and famous scientists at the reception. While Mel is off changing, however, an alarm on the console indicates the presence of a kink in Time, and the Doctor hears a distorted voice crying out for help. The voice stops before Mel returns to the console room, and the Doctor decides not to worry her about it. The TARDIS then materialises in John’s study; he’s washing up in the kitchen, and thinks that the odd noise is coming from the stereo system. He is delighted when Mel greets him, and after a happy reunion, he sets off to change and take her to the reception. While the Doctor befriends John’s cat, Jupiter, Mel explains that John works for the Foundation; he’s a historian who dabbles in chemistry, doing carbon-dating and other classified research. Their family owns this house, and John is thus permitted to live in the upper floors.

John offers to give Mel and her friend a tour of Hallam Hall before the reception. The house has been in the family for 300 years, but John’s father found it too large for the family and leased it out to the Foundation. John lives in the old servants’ quarters, and what was once the drawing room is now a reading room for the Foundation’s library. Some parts of the Hall have a reputation for being haunted, and though Mel scoffs at these stories, the Doctor takes an interest, as the ghost stories could be related to the kink in Time he picked up earlier. According to John, many independent witnesses have seen a young woman wandering the upper storeys, claiming to be trapped; this could be Eleanor Hallam, a mysterious woman who lived from about 1760 to 1811. Little is known about Eleanor; her relationship to the family is unclear, and some historical sources claim that she spent her life in the Hall and was buried in its grounds. Mel still doesn’t believe the ghost stories, and the Doctor concludes that if there is an apparition, it’s harmless enough; he’s still interested, but will put off a tour of the upper storeys until after the reception. On their way out of the drawing room, Mel sees a portrait of her ancestor, Henry Hallam, with another woman; it is not his first wife, Jane, but Henry isn’t sure whether it’s Henry’s second wife, the mysterious Eleanor, or both.

At the reception hall, the Doctor strikes up a conversation with Munro, an old friend who once worked with the Doctor on a classified research project. Mel takes the opportunity to ask John more about their family history, and John offers to show her his notes on the subject after the ceremony. He explains that Munro is going to bury a time capsule, constructed from a new alloy developed at the Foundation. Mel decides that the ceremony sounds rather dull to her, and John sympathises and hands her the key to his rooms so she can slip away and read his notes. He also tells her that he’s keeping the prototype of the time capsule canister in his rooms; she might find it interesting, as the alloy has some unusual properties and the prototype was a little unstable.

Munro delivers his speech, and the press and dignitaries then move outside to watch the burial. Munro places the last item, a selection of rare plant seeds, into the capsule and then prepares to bury it, but as he removes the last shovelful of dirt from the hole he finds something already buried inside. Rachel quickly collects it and takes it away so as not to distract the press from the main story, but the Doctor and John spot her and decide that this is much more interesting than the ceremony itself. John stops Rachel and offers to take the object off her hands, and he and the Doctor take it back to John’s laboratory. There, they conclude that it’s a 250-year-old wooden chest, and as the Doctor sets about trying to open it, John takes a sliver of wood and places it in his carbon-dating machine to confirm the dating.

Mel recovers, disoriented, to find that the study has changed subtly; it’s still the same room, but with slightly different furnishing and windows. A housekeeper named McGregor finds her and demands to know how and why she entered the house, and when Mel is unable to explain herself, McGregor insists that she visit the master to account for her arrival. As Mel accompanies McGregor through the house, she realises that it’s changed since her tour, and when she questions the housekeeper, she learns that this is the year 1781. Puzzled, Mel nevertheless decides to take the opportunity to chat with her ancestor Henry Hallam while waiting for the Doctor to come to her rescue.

The Doctor explains himself to John, who is astonished but accepts that the Doctor is telling the truth. The Doctor admits that he didn’t warn Mel about the kink in Time, as he had no idea it could pose a danger to her. He now theorises that the unstable prototype canister, constructed from an alloy the Foundation developed for the space programme, interacted catastrophically with the TARDIS due to their proximity. When he enters the TARDIS, he finds that the telepathic circuits have shorted out, damaging the console. Presumably, the TARDIS tried to warn Mel of the danger, but in doing so it interacted with the canister and threw it and Mel back to whatever era of history she had in her mind at the time. The Doctor and John go through the notes that Mel was reading and conclude that she was likely thinking about Eleanor Hallam; unfortunately, little is known about the mysterious woman apart from her arrival at the house in 1781 and her death in 1811. Some sources claim that she was confined to the house, and although Henry Hallam’s journal notes her arrival at the house on 12 December 1781, all of the pages relating to 1782 have been removed for some reason. The Doctor, concerned by the fact that the canister was subsequently buried in the grounds for nearly 250 years, decides to visit the date in question. John insists upon accompanying him, as Mel is his niece and he’s familiar with the time period; the Doctor reluctantly accepts his help, but draws the line at taking along the cat.

McGregor informs her master, Henry Hallam, that a strange young woman is wandering the house. Mel claims to be a friend of the family, and as Henry has never met her, he assumes her to be a friend of his late wife, Jane. Henry didn’t take the time to meet Jane’s friends while she was alive, and he seeks to make amends for that now; however, when he asks Mel her name, she realises that she can’t remember. She is beginning to feel dizzy, and Henry urges her to sit down and take tea with him while she recovers; he has had few visitors since Jane’s death, and is happy for the company. He sends McGregor for the tea, and she does so reluctantly; she cares deeply for Henry and is unwilling to leave him alone for long with the newcomer, fearing that the young woman intends to take advantage of his hospitality and perhaps even rob him.

Though Mel is still having trouble remembering her name and how she came to be here, she finds to her surprise that she knows a great deal about this building and about Henry himself. Henry is taken aback when Mel quotes his journal almost word for word, describing his and Jane’s grief at their inability to bear children, but Mel can’t explain her strange insight. As her disorientation grows, she becomes even more frantic, until Henry finally calls in McGregor and asks her to send to the village for Dr Michael Wallace. Mel suddenly remembers that she was waiting for a doctor, and she pushes past McGregor, running towards the study in the confused belief that this is where the Doctor will be looking for her. However, she is unsteady on her feet, and she trips and falls down the main staircase, banging her head. Henry and McGregor take the concussed Mel back into the drawing room, where Henry plies her with brandy and smelling salts while McGregor sends a messenger to the village. Mel remains confused and disoriented, and in her fragile and vulnerable state, she reminds both McGregor and Henry of the late Jane.

The Doctor sets the co-ordinates for 12 December 1781, warning John that unprotected travel through the Vortex could have serious side-effects for Mel, such as disorientation and confusion. The TARDIS encounters severe turbulence caused by the unstable canister’s journey through the Vortex, but despite the rough journey, it finally materialises in the grounds of Hallam Hall, and the Doctor and John emerge to search for Mel.

Though Henry fails to understand the reason for Mel’s distress, he takes pity on her and insists that she remain at Hallam Hall until she has fully recovered. Mel refuses to leave the study until the Doctor returns for her, and becomes frantic when Henry and Wallace try to usher her out, until Wallace resorts to sedating her with a dose of ether. He questions the wisdom of Henry taking on such a burden while he’s still grieving for the loss of his wife, but Henry is adamant, and Wallace bows to his friend’s evident compassion.

As the Doctor and John approach Hallam Hall, the Doctor senses that something’s not quite right, but he fails to connect this feeling to the warm summer weather. In fact, six months have passed since Mel’s arrival, and it is now June 1782. Wallace has returned to check on his patient, who has experienced occasional periods of lucidity but only makes sense when dosed with laudanum. Henry has been unable to identify his visitor, and Wallace suspects that her family, unable to cope with her madness, dropped her off at the Hall in order to take advantage of Henry’s good nature. However, Henry believes that “Nell” was a friend of Jane’s, which would explain how she knows so much about the family. Wallace again urges his friend to commit Nell to an asylum, but Henry, who believes that tending to Nell has helped him to bear the loss of his wife, refuses to surrender his new ward to the care of strangers.

The Doctor and John arrive at the house, and when McGregor answers the doorbell, the Doctor introduces himself and claims that John is his valet. The Doctor sends John off with McGregor while he speaks with Henry and Wallace, claiming that his young ward, Melanie, wandered away from her coach earlier today and may have ended up in the grounds of Hallam Hall. Henry and Wallace claim to have had no other visitors today, but Wallace then asks if the Doctor would mind giving his medical opinion on a troublesome patient, a delusional young woman whom Wallace has been unable to cure. Henry is wary of trusting Nell to a stranger, and when the Doctor asks whether the young woman is Henry’s wife, Henry unthinkingly responds “not yet.” The Doctor, curious, agrees to see the patient and offer a second opinion.

In the kitchen, John shares tea and conversation with McGregor, who is obviously very fond of Henry; she’s been his housekeeper for 14 years, and both she and Henry have lost their spouses. But their growing closeness changed when Eleanor arrived at the house; for the last six months, the young woman has been confined to an upper room while Wallace treats her delusions. John, realising that he and the Doctor have arrived six months too late, becomes disturbed when McGregor claims that Eleanor appeared as if from nowhere and that nobody has been able to identify her; however, he doesn’t have the opportunity to tell the Doctor of his suspicions.

Henry and Wallace lead the Doctor to the upper rooms, explaining that their patient becomes confused and disoriented if allowed to wander freely. When the Doctor enters “Nell”’s room, he and Mel recognise one another instantly, but while the Doctor plays along and greets her as Nell, Mel is dazed and disoriented and begs him to take her back home. As she grows frantic, the Doctor has little choice but to let Wallace give her another dose of laudanum to calm her down. She sinks into despair, leaving Wallace puzzled by her sudden deterioration; he thought that they’d managed to convince her that her talk of travelling through Time was a delusion. The Doctor suggests that he might be able to get through to her if they are left alone, and though Henry is unwilling to do so, Wallace is desperate enough to try anything at this point, and Henry gives in when Wallace insists that the only other option would be to commit Nell to an asylum.

Once Henry and Wallace have withdrawn, the Doctor drops his charade and wakes Mel, who is having trouble concentrating and now half believes herself to be named Eleanor. The Doctor gives her a pill he picked up as a hangover cure from Zanthas IV, frustrated by his failure to save her from this; because of the damage to the console and the turbulence in the Vortex, his friend has been stuck in this era for months, suffering from treatment for an illness she doesn’t have. The Doctor assures Mel that he’s really here and that he’s really going to take her home, but first he must deal with the unstable canister before it causes any more trouble. He advises her to rest and recover, but she’s still disoriented and begs him not to leave her. Despite her pleas, he reluctantly withdraws and locks the door to her room to keep up the charade.

Henry is having second thoughts about leaving Nell alone with a stranger, but Wallace is growing ever more concerned about Henry’s fixation on curing Nell. The Doctor then arrives and announces that the patient seems well enough, apart from the effects of being dosed with laudanum. Wallace takes offence at the Doctor’s tone, and scoffs when the Doctor suggests that instead of doping up his patient he should have listened to her and tried to reconcile her reality with his own. However, the Doctor insists that he can cure Eleanor, and to Wallace’ disgust, Henry seizes upon this slim hope and agrees to let the Doctor do what he can, throwing away months of Wallace’ hard work on the word of a visiting quack. Tempers flare, and Wallace openly accuses Henry of being motivated purely by his selfish desire to cure Eleanor so she will fall in love with him. Henry is equally enraged when the Doctor claims that he must remove Nell from Hallam Hall in order to effect his treatment, and accuses him and Wallace of consorting together to trick him into parting company with Eleanor. The Doctor and Wallace both insist that this is not the case, but Henry kicks them both out of the hall, ignoring the Doctor’s appeals to let him take Mel away for treatment.

Upstairs, McGregor speaks with Mel, who is feeling much better now that the Doctor’s hangover cure has undone the effects of the laudanum. Her memories are still unclear, but she insists that fresh air and conversation will help to clear her head. She is embarrassed when McGregor admits that she became violent after her arrival, which is why she was locked up in this room and dosed with laudanum; unsurprisingly, she can remember little of the following six months. Now confident that her ordeal is over, she tells McGregor that she travelled back in Time from the 21st century by accident, and that the Doctor has finally returned to rescue her. But McGregor laughs, believing that “Nell” is teasing her, and claims that the doctor who visited the Hall earlier has now left. Henry then arrives, having overheard McGregor’s laughter, and is delighted to see that “Nell” is feeling better. However, when she asks to see the new doctor, Henry claims that he’s gone and will not return. As “Nell” seems to be well again, Henry asks her to dress for a walk in the grounds, and as he and McGregor leave, the worried Mel wonders what the Doctor is playing at.

At Henry’s request, Mel joins him for a walk through the grounds to the summer house. On the way, she asks him whether anyone else arrived at the house in the winter of 1781, and is disturbed when the answer is no; if Henry was busy caring for her, does that mean that Eleanor Hallam was turned away? Rather than answer awkward questions, she claims that her memory has not returned, but assures Henry that her mind is now much clearer; however, she is shocked when he responds by proposing to her. He claims to have fallen in love while tending to her during her illness, but she’s put off by the realisation that he watched her sleep while she was too doped-up with laudanum to realise it. When she turns him down, he frostily reminds her that she might find it difficult to retain her honour should she leave his house now. Claiming that she is obviously still confused, he sends her back to her rooms to think over his proposal. She is unnerved by this revelation of his true colours -- and as she returns to his rooms, she realises that if she marries Henry while he believes her name to be Nell, then she will become Eleanor Hallam.

Henry returns to his drawing room, where he orders McGregor to send a letter to Wallace dismissing his services. Realising that McGregor is concerned, Henry urges her to speak openly, but he scoffs when she questions whether Eleanor is only pretending to have forgotten her past in order to take advantage of Henry’s hospitality. Henry insists that Nell cannot be deceiving him, and casually reveals that he intends to make her his wife. He then dismisses McGregor, who departs, shattered but trying not to show it.

The Doctor and John refuse to abandon Mel to her fate, and Wallace agrees to help them, as he now understands that Henry never recovered from the loss of his wife and has become deranged after pouring all of his energy into caring for Mel. The Doctor sends John to rescue Mel, and asks Wallace to dig a hole in the gardens so they will be able to bury the canister where it is to be unearthed in 2003. Wallace does not fully understand these instructions, but agrees to do as the Doctor asks. The Doctor and John then return to the house, where they find McGregor weeping in the kitchen. Though surprised by their return, the vulnerable housekeeper opens up to them and confesses her own feelings for Henry. The Doctor and John reveal that they’ve come to take Nell, or rather Mel, away from the house for good, explaining that it’s taken them a long time to track her down here. McGregor, delighted -- at least partly for Mel’s sake -- takes John to his niece, while the Doctor uses his time sensor to locate the errant canister. He finds it still in Henry’s study, but Henry catches him and throws him out of the house again, threatening to take sterner measures should the Doctor defy him and return again. Fortunately, the Doctor has the canister, and will have no need to return.

Mel is delighted to be reunited with her uncle John, but before she goes, McGregor presents her with a gift from Henry: a dress that he’d asked McGregor to pick out for her. Mel recognises it at once, and gives it to McGregor, as they’re about the same size. John urges McGregor to take the initiative and show Henry how she really feels, and McGregor, touched, gives Jane’s old sewing box to Mel as a memento of their time together. John recognises the chest and urges Mel to take it, and she and McGregor part on good terms. Outside, they are reunited with Wallace and the Doctor, who places the canister in the sewing box and gives it to Wallace to bury. Mel fears that the Doctor can’t afford to take her away from Hallam Hall without changing history, but the Doctor reminds her that there’s no solid evidence to suggest that Eleanor Hallam ever existed for any period outside these six months. John had always assumed that the family had hushed up having a madwoman in their ancestry, but the Doctor now believes that the record of her death in Henry’s journal was purely symbolic, indicating that her had finally let her memory go. Mel is starting to feel disoriented again due to the proximity of the canister to the TARDIS, but Wallace finishes burying it and bids the others goodbye, promising to tell nobody of these events. As the Doctor, John and Mel return to the TARDIS, Wallace returns to Hallam Hall, now understanding that he’s been treating the wrong patient all this time, concentrating on Mel when he should have been dealing with Henry.

Despite McGregor’s nervousness, she dons Mel’s dress and enters the drawing room to tell Henry that he’s making a mistake; Eleanor does not love him, but there is another who does. Henry angrily accuses McGregor of jealousy and attention-seeking; he will overlook this incident for the sake of her years of good service, but advises her not to speak of this again. He then orders her to fetch Nell for dinner, and is horrified when McGregor reveals that she has gone. The frantic Henry rushes up to Nell’s room only to find it empty, and when McGregor claims that her family arrived to take her away, Henry insists that he is the only family that Nell needs. Enraged, he attacks McGregor, accusing her of turning Nell over to strangers so that she could take Nell’s place in his affections. Wallace arrives just in time to save McGregor, and Henry collapses in tears, finally suffering from the complete emotional breakdown that’s been pending since Jane’s death. Wallace and McGregor vow to tend to him and ensure that he recovers fully.