Tom confronts Peter, who attempts to drug him. This provokes Hyde to appear and take Peter and Claire hostage. Claire argues that they need to find a cure for Tom's condition. Hyde kills Benjamin. Peter says that Klein and Utterson have had a cure for a long time. Tom is captured and locked inside a metal coffin.
Katherine and Miranda confront Peter, claiming they know the truth about Tom. Miranda thinks that Klein and Utterson have access to cloning technology and that Tom is Jekyll's clone. Peter denies this and orders them taken away to be killed.
Peter reveals to Claire that Tom's treatment will make him into one persona. If it is Hyde, he will be kept for research. They will make the potion that turned the original Jekyll into Hyde. If it is Tom, she will be free to take him home. When the box is opened, Hyde is dominant.
In a flashback triggered by genetic memory, Hyde has a vision of a meeting between Jekyll and Robert Louis Stevenson, the author of "Strange Case of Dr Jekyll and Mr Hyde". Stevenson agrees to write a fictional version of Jekyll's case but reveals that he knows the truth: there is no potion. Instead, Jekyll was transformed into Hyde by his love for Alice, a maid within his household. Flashbacks into Tom's own life show his Hyde first appeared during a seaside holiday with Claire, after the pair were accosted by hooligans.
Enraged by further threats to Tom's family, Hyde escapes from Klein and Utterson. Ms. Utterson, a ruthless redheaded American woman at the head of Klein and Utterson, takes Claire and her sons hostage at a private estate. She locks the twins in miniature versions of the coffin used on their father.
Tom's alleged mother, Sophia, appears on the premises and helps Claire escape her locked bedroom. She tells Claire how Klein and Utterson had tried to clone Doctor Jekyll but had been unsuccessful. Claire meets several of the failed attempts in the basement of the building. They are disfigured and in a near-vegetative state. Sophia explains that Tom is a descendant of Doctor Jekyll, through Mr Hyde, and by chance "a perfect throwback, a chance in a million". Klein and Utterson had discovered this and had watched him from when he was six-months-old. In order to trigger his transformation into Hyde, they created a clone of Alice, the maid whom Jekyll had loved. This clone is Claire herself.
Hyde tries to rescue Tom's family from Klein and Utterson. He kills Peter. There is a stand-off, with Tom and Claire's sons held hostage and suffocating. The Hyde personality is apparently killed when he is shot with multiple bullets and then manages to avoid 'sharing the damage' by taking the wounds onto himself while allowing Tom to assume his undamaged, healthy form, leaving Doctor Jackman as the only personality.
Six months later, Tom has tracked down Sophia, the woman who claimed to be his mother. When he questions her about his father, she reveals that she is the descendant of Hyde. He had inherited the family curse from her. As Tom watches horrified, the powerless, tired, grey-haired Sophia transforms into her own version of the Hyde persona, the red-headed Ms Utterson.
Jeffrey Tayor of Stagescreen Productions had the idea of a modern version of "Strange Case of Dr Jekyll and Mr Hyde" in the mid-1990s. He attempted to get it produced in the United States, but all three attempts fell through. He returned to England and joined with Hartswood Films when Elaine Cameron was looking for ideas for a supernatural thriller. Cameron approached Steven Moffat for a script. A six-part series was commissioned by the BBC's Jane Tranter and John Yorke in November 2005.
BBC America gave co-production funding in March 2006. The producers regularly met with Moffat for brainstorming sessions. The producers invited Moffat to "write anything", with the intention of cutting the material back later. However, they were reluctant to cut material once they saw it on the page. The first episode starts with Jackman already knowing about his alter ego. Because the plot of "Jekyll" begins after the story has developed for the characters, Nesbitt says that the show feels like it is a second series.
Moffat explicitly describes the series as a sequel, rather than an adaptation. He said the Jekyll of the original story really existed, and Jackman is his "modern-day descendant dealing with the same problems". As "Jekyll and Hyde" is such a well-known phrase, Moffat labored over what to call the series, eventually deciding upon "Jekyll" because that word "carries the name Hyde". The final episode replaces the title "Jekyll" with "Hyde". Producer Elaine Cameron says the one word title gives the series a "very modern feel". Moffat initially named the character Jekyll rather than Jackman, but found it cumbersome to constantly explain that the book had not been written in this alternate universe. Instead he chose a version where the book exists, but changed the name to Jackman. Otherwise, Cameron felt, the character would appear stupid by not realising what was happening when turning into Hyde.
The scene between Tom and Katherine was expanded slightly in the sixth episode to keep their relationship active to facilitate a second series. However, no further episodes were commissioned. In an August 2007 interview, Moffat told Alan Sepinwall of "The Star-Ledger" that he had a sequel written for the miniseries "should the BBC be interested".
Following "Jekyll," Moffat became a co-writer on "Sherlock."
James Nesbitt and his agent attended a meeting with Jane Tranter in late 2005 regarding the 2006 series of "Murphy's Law". At the conclusion of the meeting, she offered him a script for "Jekyll", suggesting that he might like the role. Nesbitt took the script role as a way of putting a distance between his previous work. The casting of Nesbitt as Tom Jackman and Hyde was publicised on 12 December 2005, but filming was not scheduled to begin until September 2006, increasing Nesbitt's anticipation to play the roles. Writer Steven Moffat said that the dual-role required a very skilled actor, and a well-known actor was necessary because it was such an expensive show to produce. The production team decided Nesbitt's two characters would be mainly differentiated over a change in performance rather than by extensive make-up because they wanted Hyde to be able to walk around in public without attracting attention.
Michelle Ryan was revealed to have been cast as Jekyll's assistant, Katherine Reimer, in August 2006. Ryan believed herself to be too young for the part, though that aspect had already been written into the character. To prepare, she consulted the Royal College of Psychiatry. Ryan dyed her hair red for the role to help differentiate her from Tom Jackman's wife. Denis Lawson was cast as Peter Syme. The actor consulted his post-graduate son for information on Syme's job.
Moffat initially doubted Gina Bellman's suitability for the role of Claire Jackman because he associated her too much with Jane Christie, the character she had played in his sitcom "Coupling". Moffat did not imagine the character to be as beautiful as Bellman, but her audition was so good that he revised his vision of the character. Bellman originally auditioned for the role of Katherine, but the producers wanted someone younger to play that role. However, Bellman said that she talked herself out of the role by arguing that there should be an age gap between Katherine and Claire to avoid Katherine becoming a threat to the wife. Bellman approached her role as if Claire had become caught up in Tom's mid-life crisis, an angle that impressed the producers.
Meera Syal was attracted to her role because Miranda was not a clichéd private detective and she thought the humour was "fresh". During the second filming block, Mark Gatiss briefly joined the cast, playing the small but important role of Robert Louis Stevenson in flashback scenes in episode five.