A 21st-century historian named Gillian Rose Petra has travelled in Time to conduct up-close-and-personal research into the early life and career of Sherlock Holmes. To this end, she joins the household at 221b Baker Street as a maid, taking the identity of a woman named Rose Donnelly who was murdered soon after travelling to London to seek her fortune. Working as a Victorian housemaid is harder than Gillian had expected -- especially as Mrs Hudson has two other lodgers, Cavendish and Corkle -- but she eventually finds an opportunity to follow Holmes out of the house as he conducts an investigation. He realises that he's being followed, but fortunately, his arrogant challenge to his unseen pursuer attracts the attention of three drunken louts out for a fight, and he's forced to flee. Later, while Gillian sets the fire in Holmes' sitting room, he mentions to Watson that he was followed by someone whose bootprints matched those on a pair he himself had thrown out some time ago. He also notes that "Rose" is limping, as if she'd worn the wrong size of boots recently; she claims that she's been on her feet all day, but fears that his suspicions have been aroused.

Inspector Lestrade has been investigating a number of rooftop burglaries, but it's another crime that hits close to home for Gillian when Mrs Hudson's pre-teen servant, Liza Murray, is brutally murdered and raped, in that order. Gillian and Watson are appalled when Holmes method-acts out a paedophile's frame of mind as a casual exercise in psychological profiling. Realising that he's gone too far, he apologises for his tactlessness, but while the young girl was relatively close to him, he nevertheless claims that he can't afford to take an interest in her murder unless someone hires him to solve the case. In a foul mood, Gillian uses her time off to dispose of the boots that she'd stolen from Holmes, but realises that she's being followed by a man with a vaguely Asian appearance. Believing that he's Holmes in disguise, she "accidentally" stabs him in the groin with her umbrella while bending over, only to find that it was someone else entirely. She returns to Baker Street mortally embarrassed.

In the guise of the widow Mrs Maria Tory, Gillian meets with her criminal contact Shinwell Jackson, who has been bribing the Holmes family servants for stories of Sherlock's childhood. Through Shinwell, Gillian learns that Sherlock's true first name is Edmund, and that his young sister Genevieve suffered from brain damage in a traumatic birth that killed Holmes' mother. Shinwell also warns "Mrs Tory" that Holmes has been inquiring about Rose Donnelly, presumably in an effort to stave off boredom. Later, Holmes apparently happens across Gillian as she busks her guitar in the park; recognising her talent, he invites her to play a duet with him when she returns. She accepts his offer, but when she gets back she realises that her rooms have been searched and that he was only trying to find out how long she'd be away. Furious, Rose tells Watson that she had to leave home after unpleasantness with a married man, and claims that she fears she'll lose her position in the house if Holmes digs up the old scandal. Watson remonstrates with Holmes, who reluctantly concedes that he has no evidence to support his unfounded hunch that "Rose" is spying on him for some reason.

Still irritated with Holmes, Gillian decides to accept when Mrs Hudson's son Jack invites her out to dinner and a show, although she knows that he's just a layabout who wants to get into her knickers. Nevertheless, she drinks too much gin and allows Jack to walk her home, which proves to be a mistake when they wander into a dark alley. Already short of breath due to her corset, she's unprepared when he assaults her; fortunately, Holmes has been following her in disguise, and he gives Jack a thrashing and threatens to press charges unless he moves to Australia immediately. The terrified Jack agrees to do so, and Holmes escorts "Rose" back home. On the way, he tells her that she is clearly anything but an ordinary housemaid and can't pretend otherwise; nevertheless, he doesn't press her for answers, as he's become intrigued and wants to solve the mystery of her identity by himself. Holmes repeats his invitation to play a duet, and this time he keeps the appointment. Even Watson is surprised by the passion that flowers between Holmes and Gillian when they begin to improvise around one of Holmes' own compositions. That night, Gillian bumps into Holmes on the staircase, and drags him into the linen cupboard before he really realises what's happening.

Their affair continues for two weeks, and although Gillian is aware that Holmes is still trying to deduce all he can about her from close observation, she deludes herself into thinking that she can use this as further material for her thesis. However, one night Holmes tarries too long in her bed and is caught sneaking downstairs by his fellow lodger, Corkle. The next day, Corkle asks to speak to "Rose" in private... and reveals that he is her fellow time-traveller, a combined pilot and navigator. Gillian's presence here was made possible by a corporate scientist named Jimmy Moriarty, and she thought he was allowing her to use his new technology to conduct first-hand research for her thesis -- but faced with Corkle's arrogant attitude, she begins to suspect that there's more to the project than she's been told.

Corkle points out that "Rose" will be dismissed from service immediately if Mrs Hudson discovers that she's been sleeping with one of the lodgers, that Gillian can't afford to retreat into the mantle of Mrs Tory permanently for fear that Holmes will find her out, and that she has no way of getting back home until the send-forward on 26 August. Corkle advises her to break off her affair with Holmes and instead conduct her research using surveillance equipment that Corkle had brought back in Time with him; he has had no excuse or opportunity to enter Holmes' rooms himself, but as a maid, "Rose" can easily plant the discreet bugs. Gillian is reluctant to betray Holmes, however -- at least until their next encounter, when Holmes coldly brushes her off, reminding her that she is his only his maidservant. He may be trying to keep his distance after allowing himself to be caught in the act by a fellow lodger; whatever his reasons, he succeeds in angering Gillian, who waits until both Holmes and Watson have gone out for the evening and then plants the thin, invisible surveillance devices in their sitting room. She and Corkle can now eavesdrop on Holmes' private conversations without any need for Gillian to get close to him.

Lestrade is still investigating the rooftop burglaries, and he greets with some hilarity Holmes' casual claim that the burglar is a lesbian trapeze artist who works as a maidservant. Holmes eventually gets an interesting commission from Lady Holbrook, whose grandson Merrill still has not consummated his nine-month-old marriage to American oil heiress Henrietta Barstow. This rather suggests that he's not interested in women. An Austrian doctor named Jacob Armitroy has apparently discovered this and is threatening to blackmail the Holbrook family; if the truth comes out, the marriage will be annulled and the Holbrooks will be forced to refund the considerable dowry. Unfortunately, Merrill himself has disappeared, and Lady Holbrook thus hires Holmes to find him and put him in touch with her solicitor, Maitland.

Corkle later goes out on business, and Holmes returns to Gillian, admitting that he turned her away for her own sake because he feared that he would lose interest in her once he'd solved the mystery of her origins. They make love again, and Gillian realises that she's fallen in love with Holmes despite herself. When he tells her that she cannot reciprocate, she is humiliated and tells him the truth, or as much as she feels she can: he's one of the first consulting detectives, a brand-new profession brought into existence by the changing socio-economic factors of history, and she's studying him for her doctoral thesis. Holmes is close to understanding the truth, but he rejects his conclusions as madness, and she begs him to leave her for both their sakes.

Holmes immerses himself in the investigation into Lord Merrill's disappearance, and in the course of his work he's propositioned by a photographer named Shamus Tiramory -- a name that catches his attention for some reason. Later, when Corkle comments to Gillian about the spring in Holmes' step, she realises that his innuendos are a bit too accurate... which implies that Corkle has planted surveillance devices in her room as well. Thinking along these lines, she realises that the names "Jacob Armitroy" and "Shamus Tiramory" are derivatives and anagrams of "James Moriarty," just like her own alias of "Maria Tory." The obvious implication is that Corkle, or another of Moriarty's agents, is responsible for the disappearance of Lord Merrill, and that the real Moriarty had an agenda other than pure historical research. Disturbed, Gillian makes a wax impression of the key to Corkle's rooms, intending to break in and investigate him once she gets the opportunity.

Some days later, while Corkle is suffering from a bout of flu, Holmes invites Gillian to accompany him to the West End; it's not exactly a date, as he's following up a lead and needs an escort and decoy. Gillian accompanies him to the Café Royal, where they run into one of Holmes' old school chums, a flamboyant homosexual named Harry Hughes. Hughes, clearly unaware that Holmes has been recently cruising the gay scene himself, asks Holmes to look into the disappearance of his friend Stewart Ronaldson. As they leave the café, Gillian realises that they're being followed and that Holmes knows it. He takes her to his real destination, an "art photographer" named Giorgi Santelli; claiming that he's there to set up an appointment for an "artistic" photograph of his consort, he also offers Santelli money for a look at the other photos in his collection. Realising what Holmes is really after, Gillian asks Santelli if there are any photographs with just boys, giving Holmes the opportunity to find and steal the photograph he was looking for.

Having succeeded in his mission, Holmes takes Gillian to a nearby café. Their pursuer enters soon afterwards, presumably under the impression that they've taken advantage of one of the café's "private rooms," and Gillian recognises him as the man she speared with her umbrella back in October. Her reaction gives her away to Holmes, and when she lies about having seen their pursuer before, he becomes angry with her. They use this as a pretext to start an argument so Gillian can storm out and Holmes can follow the strange man, but in her irritation she takes a wrong turn, and while trying to find her way back, she slips on a patch of ice and hits her head. She is thus too dazed to fight off her stalker when he shows up to offer his "assistance." Fortunately, the stalker also slips on the ice, and Gillian is able to evade him until Holmes shows up and drives him off. Holmes helps Gillian back to 221b Baker Street, where he tells Mrs Hudson that he found her after she slipped on the ice just outside the house. Gillian doesn't tell Holmes, but she suspects Corkle of setting up the attack.

On 10 March, Holmes receives a distressing telegraph, and shortly afterwards, his brother Mycroft visits him. Corkle records the conversation, and when he and Gillian listen to it later, they learn that Holmes' father has died and that Sherlock feels guilty that he doesn't care. Mycroft reminds Sherlock that he has a duty to their sister, and Sherlock reluctantly departs to attend the funeral. In his absence, Gillian contacts Shinwell Johnson and asks him to copy the key to Corkle's rooms -- but Shinwell warns her that she's being watched by inspectors from the CID. Concerned, she agrees to break off communications with Shinwell, but asks him for one last favour: to find out all he can about a Jacob Armitroy and a Shamus Tiramory, and send the information to Sherlock Holmes.

The next day, Gillian gets an opportunity to break into Corkle's rooms, where she finds a CD-ROM hidden inside his copy of Alice in Wonderland. When she plays it back on his camcorder, she's horrified to see that he recorded himself torturing and molesting Stewart Ronaldson and the dead body of Liza Murray. She has little time to react to this horror before police suddenly burst into the house and arrest her, responding to an anonymous tip; when they search her rooms, they find evidence that connects her to the burglaries that Lestrade had been investigating. Gillian is thrown into prison, and Corkle visits her, claiming to be her solicitor. However, he's unaware that she's learned his secret; he merely framed her for the burglaries because her affair with Holmes threatened his own agenda. Corkle warns her to cut off all contact with Holmes and wait quietly until it's time for them to go; otherwise, Corkle will let her rot in prison until it's time for the send-forward in August.

Before Gillian can decide what to do, Holmes returns to London, learns of her plight, and informs the police that the real rooftop burglar was a former Romanian trapeze artist, Carolina Lopenski. He had identified her some time ago, but didn't care to inform Lestrade, and now fears that his arrogance has led to Carolina's murder by whomever intended to frame "Rose Donnelly." As proof, he brings in a window of the same dimensions as those the rooftop burglar has easily wriggled through in the past, and has Gillian demonstrate that her hips are too wide to fit through. The police have no choice but to release Gillian, but Mrs Hudson refuses to let "Rose" back into her house, as Corkle and Cavendish have already left due to the scandal. Holmes escorts her to Maria Tory's house, only to find that it's been closed down and all the possessions removed, presumably by Corkle's associates.

As Gillian has nowhere else to go, Holmes takes her to Harry Hughes' house, where she succumbs to shock and drinks herself into a stupor. Holmes then returns in a fury, claiming that his pocket was picked in the street and that the thief took the shattered remains of the silver disc he'd found in Gillian's rooms -- the CD-ROM containing proof of Corkle's crimes. Holmes misinterprets her reaction to this news and loses his temper, demanding to know what she's hiding from him; drunk and angry, she attacks him, and is seriously injured when he pushes her aside. Mortified, he takes his leave and later sends her a letter, telling her that he's let his heart overrule his mind; he must cut off all contact with her and find out who is trying to set this trap for him. By now, Gillian has recovered enough to realise that he's making a serious mistake; he thinks she was the bait for the trap, but Lord Merrill was the real bait and she was a distraction that prevented him from taking it. Without her to stop him, Holmes will walk right into whatever trap Corkle has set for him.

Despite Holmes' attempts to avoid contact, Gillian and Harry eventually track him down to the Belvedere Club, where he's pursuing his investigations by flirting with a man named Evelyn. Gillian manages to convince Holmes that she has important information that could help him to save people's lives, and he reluctantly agrees to meet her the next day. Harry has picked up another man, and Gillian thus agrees to walk home with a woman named Iris, whose cousin Nigel has likewise deserted her. They bump into Watson on the way out, and although he's supposed to be helping Holmes, he gallantly offers to escort the women home. Iris seems peeved by this, and Gillian assumes that this is because Iris intended to proposition her -- but when Watson leaves, it turns out that Iris was leading Gillian into a trap set by Nigel and "China Crow," the stalker who nearly kidnapped Gillian once before.

Watson hears Gillian's cries for help and rushes back to the rescue -- but he can't bring himself to shoot a woman, and Iris thus shoots Watson in the leg and orders the thugs to take him as well. The thugs imprison Gillian and Watson in a dark dungeon cell, where Corkle visits them and explains that he needs to keep Gillian alive because she has a tracing implant in her arm that will enable him to get home. He'd hoped to get her safely out of Holmes' way by having the authorities lock her up, but since Holmes returned too early from his father's funeral and got her out of jail, Corkle has resorted to more desperate measures. Gillian realises that Corkle was responsible for Holmes' father's death, and that he'll have no compunction about killing Watson if he deems it necessary. Nevertheless, Corkle has no reason to kill Watson just yet, and he provides basic medical supplies so Watson can patch up the wound in his leg.

Days pass, and Watson and Gillian lose all sense of time. Desperate for human contact, Gillian tries to have sex with Watson, but he refuses -- and reveals that Holmes really is in love with her and wept on the night he thought she'd betrayed him. However, he then tells Gillian that Holmes entered the sitting room and loudly announced his intention to cut off contact with her, and she realises that Holmes was trying to be overheard in order to lure his enemy into a trap. Fired up by this spark of hope, Gillian and Watson try to escape the next time their captors bring food, but they fail, and Crow viciously beats Watson to within an inch of his life and takes him away, leaving Gillian alone in the darkness. More days pass, and eventually Crow decides that Gillian is far enough gone that he can rape her without Corkle knowing. But as he's doing so, Holmes finally arrives, overpowers Crow and his associate Ben, and locks them both in the cell. He apologises for failing to find her earlier, and Gillian, still in shock, tells him to leave Crow in the darkness to suffer. Before leaving, Holmes picks another lock and finds the dungeon in which Corkle videotaped the atrocities he'd committed -- and Gillian faints upon seeing that there are still bits and pieces of Stewart Ronaldson, Merrill Holbrook, and Liza Murray preserved like relics in the cell.

Holmes takes the traumatised Gillian to Middlesex Hospital, where she defies the Victorian doctors' conviction that she'll never recover from her experiences. She is eventually discharged and returns to 221b Baker Street, where she finds Holmes preparing to leave on a journey. All evidence of Corkle's atrocities had been removed from the dungeon by the time he returned with the police, and Crow and Ben had been killed with poison gas. Due to Watson's absence, Holmes was unable to spring his trap on T. Evelyn Wickford, the man with whom he had been flirting at the Belvedere Club; Wickford turned out to be a dead end, and his wife has named Holmes in her divorce proceedings. Due to this scandal and his inability to prove the death of Merrill Holbrook, Lady Holbrook's solicitor intends to prosecute Holmes for fraud. Liza Murray's father then bursts in to confront Holmes over his failures, but apologises for his harshness when he sees Holmes' clear distress. Holmes promises to follow Liza's killer to the ends of the earth -- and beyond, if necessary.

Gillian faints upon learning that Corkle has fled the country, taking with him her only way home. When she recovers, she tells Holmes the entire truth about herself and her journey back through Time. She was only interested in conducting research, but she has come to understand that Moriarty and Corkle are conducting an experiment to see if it's possible to change history by destroying the life of a single famous man. Holmes deduces that Gillian was sent back because she'd already been researching his life; as an expert, she would easily be able to tell whether history had changed when she returned "home." He reveals that he's received a scrawled message from Watson implying that his kidnappers have taken him to Java on a sailing vessel called the Hope, and Gillian insists upon accompanying Holmes, explaining that Krakatoa is due to erupt on 26 August -- the event that was to provide the energy that would send her and Corkle back home.

Holmes and Gillian travel to Java as husband and wife, and arrive ten days before the eruption. Undercover, they learn that a sailor aboard the Hope was paid to throw two trunks overboard shortly before docking; hopefully, they contained Corkle's video equipment and not Watson. Holmes vanishes while following this lead, and Iris and Nigel show up at Gillian's hotel and take her to a nearby villa where Corkle is waiting. He is shocked to learn that Holmes very nearly set off for Java without her, but recovers and reveals that Watson is being held in Telok Betong. The island's prison is due to survive the eruption, but Corkle refuses to move him there unless Gillian plays along with him. Gillian reluctantly agrees to do so, and Corkle thus allows her to visit Holmes, who has been chained up in a nearby hut. Holmes admits that he expected Corkle to come for Gillian, but wasn't expecting to be captured himself. Gillian is forced to tell him that Watson is dead, but as she leaves, she sees that he's been trying to dig free the beam to which he's been chained.

Since it appears as though Corkle has won, he sends the telegram to Telok Betong as promised on the morning of 24 August, arranging for Watson to be moved to a safe location. On his way back to the villa, he admits to Gillian that Moriarty did not develop time-travel technology on his own; rather, it's a technique or ritual taught to him by beings called the Celestial Host, sentient ideas that need minds to live in and thrive on grand guignol and horror. It's possible that Moriarty didn't know the extent of the evil that Corkle would commit in his name, but that's why Corkle used anagrams and derivatives of Moriarty's name; now the scientist's hands are bloodied as well. Corkle and Gillian return to the villa, but find that Holmes is missing. Enraged, Corkle sends his thugs out to search the jungle, but once the coast is clear, Holmes arrives with a pistol that he claims Nigel has no further need of. He releases Gillian, who nearly kills Corkle in a fit of rage but then calms down and stops Holmes from doing the same in cold blood. Holmes and Gillian tie up Corkle and flee, but Gillian tells Holmes that they must go their separate ways; he must rescue Watson, and she must return to her home time and make sure that Moriarty pays for what he's done.

Holmes insists upon accompanying Gillian to the machine that will send her home, but Corkle and Iris track them down on the way. The furious Iris tries to kill Holmes for murdering Nigel -- who was her cousin, sibling, lover, or some combination of the three -- but Gillian stands between them, and Corkle is forced to shoot and kill Iris before she can fire, as he still needs Gillian alive. Corkle is unused to this era's pistols, which take time to reload, and Holmes manages to overpower him and take the gun. However, Corkle then informs Holmes that he merely staged obscene tableaux with the dead red-haired girls in order to pique Holmes' interest in the case; they were really murdered by a madman named Francis Black, and before leaving England, Corkle arranged for Black to be employed at the asylum where Holmes' childlike, red-haired sister Jenny was committed following their father's mysteriously convenient death. Holmes, pushed to breaking point, demands to know why Corkle has done this -- and when Corkle reveals that he did it simply because he could, Holmes shoots him in the head.

This act has nearly broken Holmes, as Nigel in fact died after falling from his horse; Corkle is the first man Holmes has ever killed. Gillian manages to bring Holmes back from the brink of madness and despair, reminding him that he still has to save Watson and his sister, and put his life and career back together despite the scandals and failures that Corkle had arranged. Holmes agrees, but nevertheless insists upon accompanying her to the hut where she and Corkle were to return. There, they find that the "time machine" is more like a voodoo ritual than a technological artefact. Gillian tears herself free of her lover, gives him her notes so that he can prove Corkle's complicity in the murders, and takes Corkle's CD-ROMs with her so she can prove the same back in her own era -- if it still exists. She then forces Holmes out of the hut as Krakatoa explodes. He is forced back into the hut when the shockwave strikes the island, but finds it empty. Nevertheless, he refuses to give in to despair, and waits out the storm; whether Gillian returns to him or not, he will return to his life and make something of it.