- "You're wrong, you know. You do count. You've always counted and I've always trusted you."
- ―Sherlock to Molly [src]
A Study in Pink
After watching Sherlock whip a corpse with a riding crop, Molly asks him if he would join her for coffee. He interprets this as her simply offering him a cup, to which he responds, "Black, two sugars, I'll be upstairs." She shrugs off this blow although she is obviously hurt by his lack of interest in her. Molly applies lipstick, aiming to impress Sherlock. He notices, though it does not have the desired effect upon him. 
The Blind Banker
Sherlock flirts with her, complimenting her hair, in order to gain access to two bodies in the morgue. This suggests he has some knowledge of her affection for him. 
The Great Game
When Sherlock is in the lab investigating the shoes of Carl Powers, Molly is seen helping him. "Jim from IT", who she is dating, enters and introduces himself to Sherlock. When Sherlock deduces that he is gay, Molly is visibly upset and yells at him. In actuality, this is all a ruse created by Moriarty to get closer to Sherlock, which failed as Sherlock was dismissive of Molly during their interaction in the lab. Upset by Sherlock's deduction, Molly leaves the lab. While Sherlock is obviously upset that he has hurt Molly, he only notices that he has done so when she runs out. 
A Scandal in Belgravia
Molly appears at the Christmas party at 221B Baker Street, dressed up nicely in a figure-hugging dress. Sherlock embarrasses her by deducing that she has a present for a boyfriend whom she is wildly in love with and will later meet that night, comparing the colour of her lipstick to the colour of the wrapping paper in order to draw attention to her lips "to compensate for the size of her mouth and breasts". It turns out that the present is for him. Molly becomes visibly upset, but Sherlock apologizes sincerely and gives her a kiss on the cheek, which visibly shocks John. At this point, Molly is the only person that Sherlock has apologized to without prompting and the only person other than Mrs. Hudson that he has kissed on the cheek. John looks on bemused by the detective's sudden change in attitude.
Molly later turns up at Bart's to analyse what is believed to be Irene Adler's corpse. She is clearly troubled by the fact that Sherlock is able to identify the naked body from "not her face". Later, she sees Sherlock analysing Adler's camera phone, which is loaded with four small explosives at the ready to blow up the camera phone. She becomes visibly insecure when Sherlock mentions that "She [Irene] loves to play games" and then proceeds to ask if she is his girlfriend to which he responds "You think she is my girlfriend because I am x-raying her possessions?". Molly then says that "we all do silly things" which then triggers Sherlock to try another passcode to Irene Adler's locked phone. Sherlock responds with, "Yes... they do." excluding Molly as well as himself from the normal "idiots" of the world. 
The Reichenbach Fall
Molly is on her way to a lunch date when Sherlock and John barge into Barts; Sherlock waves two packets of Quavers at her and says he is taking her to lunch, and she willingly helps analyze the linseed oil discovered at the kidnapping scene. She brings a large stack of books into the lab and analyzes the material from the shoe print under another microscope, listing out figures for him. Sherlock thanks her but calls her "John". She looks visibly upset and corrects him, but he only responds with "Yes." This was not meant as an insult; it was a slip and shows that in Sherlock's mind, Molly on the same level as John, his best friend. He often forgets other names– notably Greg Lestrade's– but the only person he ever mistakes for John is Molly. This shows his strong trust in both her medical knowledge in the lab and during postmortems as well as her companionship.
In a mostly one sided conversation, she attempts to speak to Sherlock about her father, who she believes was similar to him, stating that when her father knew he was going to die, he was only sad when he thought no one could see him, and that Sherlock acts the same when John is not looking. When Sherlock states that she can see him, she says simply that she does not count and offers him help if he needs it. Sherlock looks surprised and confused at her reply and watches her walk out of the lab to purchase some crisps.
Later, after being discredited, Sherlock immediately goes to Molly and startles her in the darkened lab. He tells her that she was wrong earlier, saying "You've always counted, and I've always trusted you." He goes on to vulnerably ask for her help, saying that he is not okay and that he believes he may die. He asks Molly if she would still help him and trust him if he was not everything the world thought he was. Molly asks several times, "What do you need?", to which Sherlock finally responds, "You." She agrees to his request and played a vital role in helping him to fake his death. 
The theme of Molly "seeing through" Sherlock is reiterated throughout later series; unlike John and Lestrade, who view Sherlock as superhuman or a "machine", or ever Sherlock himself, who constantly refers to himself as a "sociopath", Molly sees him as he is: flawed and human. This may be why Sherlock approached her for help in faking his death instead of John. He did not want John to think less of him or see him as vulnerable, but knew that Molly's opinion of him would not be changed and that she would be more than happy to help him in his time of need.
The Empty Hearse
Molly first appears in a visualization of one of Anderson's theories. Anderson believes that Sherlock survived the fall from the Barts rooftop with the use of a bungee cord, which pulled him back just before he could hit the ground. Several floors above, Molly watches Sherlock fall. She then stumbles back, startled, when Sherlock crashes through the window and removes the bungee cord. Without a word, Sherlock flips his coat, ruffles the glass out of his hair, and passionately kisses Molly for a few seconds before pulling away and leaving St. Barts. In Anderson's plan Molly also would have helped transform the body of Jim Moriarty into a Sherlock look-alike.
Two years after Sherlock's apparent suicide from the roof of St Barts, Sherlock and Molly reunite in the Barts hospital locker room. When Molly sees Sherlock standing behind her in a mirror, she smiles softly and turns to face him.
Later, after Sherlock returns to detective work, he calls Molly to be his assistant as he is at odds with John, who is upset that Sherlock faked his death and did not tell him. He calls Molly around to Baker Street and nervously asks her to solve crimes with him. However she thought that he was going to ask her for dinner. They then accept clients, with Molly asking if she should take notes like John does. Sherlock responds that Molly is not being John, she is being herself. Molly smiles.
Throughout the day, Molly acts quite different from how she used to, being more confident and speaking to Sherlock without stuttering. Molly is seen investigating with Sherlock at Anderson's faked crime scene, where she quickly deduces the age of the skeleton propped up at the desk. After Molly says this, John's voice in Sherlock's mind leers, "jealous?" This could refer to Molly's intelligence or her engagement to Tom, which he has surely deduced by this point in time. Molly is also with Sherlock when Mr. Sholcott shows them the video footage of the disappearing underground car. When Sholcott explains that his girlfriend is a big fan of Sherlock's, the detective asks "girlfriend?" in surprise and snorts. Molly elbows him and shoots him a glare, which leads to him quietly apologizing. This is the continuation of a theme throughout the show that Molly is the only person who Sherlock directly apologizes to or can make Sherlock sincerely apologize to someone else.
When Sherlock asks Molly to go for fish and chips, she dodges the question and asks what today was about. Sherlock said that he wanted to thank her for everything she did for him and that Moriarty made a mistake when targeting his friends, as he had forgotten about Molly. To him, Molly was the "one person who mattered the most" and Moriarty had erred thinking that she didn't matter at all to him. Molly says that she would love to solve crimes with him again but is unable to because she is engaged. He congratulates her and says that he hopes she will be very happy and that she deserves it. Molly states that she met Tom through friends (not at the office, unlike "Jim", who was Moriarty pretending to be an IT worker) that he has a dog, they go to the pub on weekends, and that she has met all of his friends and family. She then says she does not know why she is telling him all of this. Sherlock teasingly says that not all the men Molly 'falls' for turn out to be sociopaths as Molly questions him saying "No?" and him slowly shaking is head replying "No.". He then smiles down at her and kisses her on the cheek before walking out of the door. She is then seen saying "maybe they're just my type", indicating that she isn't truly over Sherlock.
When Molly arrives at 221B Baker Street later in the episode along with Tom, it is clear that he reminds her of Sherlock due to his appearance. Sherlock and John notice but say nothing. Lestrade asks if it is serious between her and Tom, and Molly happily claims she has moved on. Molly seems oblivious to the fact that Tom is very similar in appearance and dress to Sherlock. 
The Sign of Three
Before the wedding of John and Mary, Molly showed nervousness about the prospect of Sherlock making a speech if he were to be selected to be John's "best man". She consults Lestrade and Mrs Hudson about it but they both reassure her it will be fine.
Sherlock comes to her for help with controlling his and John's alcohol levels on Stag Night so that they do not get too drunk. Molly points out that he is a graduate chemist, meaning that he could easily do it himself, but Sherlock respond by telling Molly that he lacks the "proper experience". Sherlock asks about Tom, to which she responds that he is "still not a sociopath" and that they are "having quite a lot of sex", which makes Sherlock feel extremely awkward.
She is a guest of the wedding along with Tom. Molly is shown giving lots of affection towards Tom but it looks a bit forced. She also cries when Sherlock gives his best man speech. Tom gives a surprising theory to a murderous case at the wedding, embarrassing Molly, who hisses for him to sit down. When Sherlock is trying to find the Mayfly Man, Tom says "he's pissed, isn't he?" resulting in Molly stabbing him in the hand with a fork.
She notices Sherlock leave the wedding early. She takes a step to go after him however, but she doesn't due to her being with Tom. 
His Last Vow
After John retrieves Sherlock, Wiggins, and his neighbor's son from a drug den, he takes all three of them, along with Mary who was driving the car, to St Bartholomew's Hospital. He calls Molly to request that she test Sherlock for drug use to which Sherlock looks worried. Molly tests him and is very angry that he has taken drugs. She slaps him three times on the face, saying "How dare you throw away the beautiful gifts you were born with, and how dare you betray the love of your friends!" and demanding that he apologize. Instead, he deduces that Molly is not wearing her ring and says sarcastically "Sorry your engagement is over." and that he is grateful for the lack of a ring. Molly knows that Sherlock is trying to upset her and she tells him to stop it.
When Sherlock is shot by Mary, Molly is seen in his Mind Palace and helps him to analyze the impact of the bullet. She directs him which way to fall- forward or backwards- and again slaps him, telling him to focus as he only has three seconds of consciousness left. Sherlock's view of her as a personification of medical knowledge in his Mind Palace shows that he trusts her advice and views her as very intelligent. The continued reiteration of her slapping him also shows that he sees her as the one who makes him right and brings him back to reality when he cannot focus, instead of him slapping himself in the face as he does in The Sign of Three.
When Sherlock goes missing, it is revealed that Molly's house was one of his bolt holes. Molly also says that Sherlock slept in her room while she had the spare because they both agreed he needed the space. This implies that Sherlock might have stayed with Molly sometime between his faked death and his return since she was one of the few people who knew he was still alive and he trusts her. 
The Six Thatchers
In this episode, it is implied that Molly and Mary Watson have a fairly close relationship, as Mary asks her along with Mrs Hudson to be the Godmother of her daughter, Rosamund Mary Watson. At Rosie's christening, she is seen telling Sherlock to put down his phone. When Mary and John are about to leave for the aquarium and realize that someone needs to watch Rosie, Mary suggests that they call Molly. After Mary's death, Molly is seen taking care of Rosie and tells Sherlock that John said he would rather have "anyone but him" offer to help with his daughter.
The Lying Detective
She does not have much screen time in this episode, however, when Sherlock is presumed to be on drugs, John says that they were calling the only person who had learned to see through his "bullish*t" a long time ago. The person who Sherlock "would least expect". That scene ends with John being quite puzzled as the door is opened to reveal Molly, who had already been called by Sherlock, thus implying she was not the last person Sherlock would think of. She is lastly seen getting out of an ambulance with Sherlock, looking a bit different from before, leading to several assumptions. When John asks how he is, Molly states that she's "seen healthier people on the slab." Angrily, she tells Sherlock that if he keeps taking "what he's taking and the rate he's taking it", he has weeks to live, if that. When Sherlock brushes her off, she is visibly upset at the thought of his death and shouts at him, "For Christ's sake, Sherlock, this is not a game!" She witnesses when Culverton Smith comes to salute Sherlock at the scene, and as Sherlock and John follow Culverton inside, Sherlock shoots one last glance at her before they go.
The Final Problem
In this episode, one of the tests Eurus Holmes puts on Sherlock is to put Molly in danger. He enters a room with a small coffin that says "I love you". He soon deduces the coffin belongs to Molly Hooper and Eurus makes him call her and make her say she loves him in three minutes, or she will blow up her apartment. Molly is in a bad mood and reluctant, so she makes Sherlock say it first, like he means it. He says it first, and ends up saying it twice. After that, he says he won, but Eurus reveals there were never any explosives in her apartment, and that he had just lost (this is implied to be a reference to the quote said in "A Scandal in Belgravia", where Sherlock says, "Sentiment is a chemical defect found on the losing side."). After Eurus hangs up, Sherlock proceeds to close the coffin, and destroys it in a very agitated state.
Molly is last seen entering the newly refurbished 221B in a very happy state, after Sherlock sent a text saying "You know where to find me." This could imply a new relationship between Molly and Sherlock, or at least an amendment of their friendship after the aftermath of the phone call.
Molly has a crush on Sherlock Holmes, which he frequently exploited to get her assistance. However this changes further inwards.
Sherlock seems to know she has feelings for him, yet remains impassive whenever she attempts to further their relationship. At times, he is quite rude to her. Sherlock seems content with remaining acquaintances and sometimes work colleagues. However, by the end of series two, it is demonstrated that he cares for her too.
As their friendship progresses, her romantic affections for him become muted, if still lingering ever-so-slightly between the two. She is the "One person that matters the most" to Sherlock. Thus probably hinting at the scene between Sherlock and Molly, when he is forced to say he loves her. 
Molly is the person Sherlock asked to solve crimes with him when John refused. It is a tricky, sometimes awkward time because she thinks that she is supposed to be John. Sherlock assures her he only needs her to be herself. At the end of their day together, Sherlock reveals he asked her to spend the day with him in order to thank her for her help in faking his death and invites her to dine with him that evening. Molly declines and Sherlock deduces the reason for this is because she is now engaged to be married. Molly explains about Tom, her fiancé. Sherlock congratulates her on finally loving a man who is not a sociopath. This, because Sherlock has labelled himself a "sociopath" many times in the past, implies that he believes he himself is not a good match for her. Before the two go their separate ways, Sherlock wishes her the best in her new relationship, saying she "deserves to be happy." Then, before parting ways with her, he kisses Molly on the cheek. 
When Molly was engaged, the dynamic between the two shifted – Molly claimed she had moved on; yet traces of her previous crush still linger. The fiancé dresses and looks remarkably like Sherlock, something everyone – including Sherlock – notices, but refuse to announce to her. It doesn't take long for her relationship with Tom is starting to signs of wear and annoyance for Molly. It is clear that, although he might look and dress like Sherlock, Tom is not half as brilliant. The engagement between the two is shown to be broken off.
When on the run, it is revealed that one of Sherlock's 'bolt-holes' is at Molly's house. At first, she states that he has stayed in her spare room. However, she awkwardly corrects herself, explaining that he, in fact, stays in her bedroom because they "agreed he needed the space". 
Jim Moriarty spared her life when targeting Sherlock's friends. It is possible Jim was not aware of the depth of Molly's importance to Sherlock. This is further implied when Sherlock claims Moriarty's biggest mistake was in not considering that Molly mattered.
We can again see Molly's importance to Sherlock when Mary shoots Sherlock in the chest. He imagines Molly in his mind palace and with her help, and a little input from Mycroft, Anderson and Redbeard, he survives the shooting. 
Their relationship changes greatly in "The Final Problem". Sherlock is forced to say to her "I love you". It is implied that the viewer may interpret this as he chooses, but many assume that it is the peak of the humanization of Sherlock, and that he probably, in fact, meant it. 
Molly and Dr John Watson do not interact much, and when Sherlock is around she sometimes neglects to remember his name. However, it is obvious that John likes Molly platonically and holds her in high esteem. This is not only for her various efforts in helping him and Sherlock solve cases, but also because of her sweet, unassuming personality. Moreover, John – aware of her crush on Sherlock as well his friend's lack of reciprocation of these feelings – feels sorry for Molly for all the times Sherlock uses her infatuation to manipulate her into doing whatever he asks. He often chides Sherlock for his behavior towards Molly and tries to make him treat her better.
Molly was a guest at John's wedding. Later, she becomes a godmother for his daughter, Rosamund Mary.
Molly and Jim Moriarty dated briefly, however she only knew him as 'Jim from IT'. After 'Jim's' attempt at giving Sherlock his phone number, she broke up with him. She describes their meeting as an 'office romance', as Jim was posing as an IT worker at the time. He did this to get close to her and, through doing so, meet Sherlock Holmes. She is furious when Sherlock announces Jim is gay, pointing out bluntly that Jim has left his number for Sherlock to call. Frustrated and humiliated, Molly tries to deny Sherlock's deductions, but is unable to do so. Near to tears, she abruptly storms off, leaving Sherlock startled and unsure of what happened. She breaks up with Jim some time afterwards. Jim then meets Sherlock and John, mocking him for falling for his act. 
Molly tries to contact him via her blog, but after she discovers his true identity she discontinues it because "it was all a lie".
Molly and Greg share a friendly relationship. He gawks at Molly's appearance, suggesting that he found her attractive, and offered her a glass of wine. However, he has not been seen expressing feelings towards her again other than that as he knows that Molly is in love with Sherlock.
Molly was engaged to Tom. She says that they met through friends. It is implied that she is attracted to him because he looks and dresses a lot like Sherlock.  They attend John's and Mary's wedding together. However, Molly is embarrassed when Tom attempts to solve the case of The Bloody Guardsman, ordering him to sit down after he suggests the weapon was a knife made of meat and bone. She later stabs him mildly in the hand with her fork when he speaks and further embarrasses her. Despite the strained appearance of the couple, they pose for photographs and dance together.  Not long after, the relationship faltered and they broke it off.
Rosamund Mary Watson
Rosamund Mary Watson is Molly's goddaughter. John and Mary Watson asked Molly, Mrs. Hudson and Sherlock to be Rosie's godparents. Molly was present at the Christening and accepted her duties as Rosie's godmother. When John and Mary have to run off to Sherlock it is Molly they call to take care of Rosie. And after Mary's death it is Molly who is taking care of Rosie, while John deals with his grief.
- Like Sherlock and John, Molly has her own blog.
- Molly states on her blog that she has a cat called Toby.
- Molly is one of the few recurring characters not based on a character from the canon stories. Steven Moffat said that Louise Brealey was "so fantastic" in the role of Molly that they broke their rule of not adding any regular characters not from the original stories written by Sir Arthur Conan Doyle .
- When asked about Molly, Steven Moffat stated that the creators of the show "often forget that they invented Molly" and see her as adding a lot of depth to Sherlock's story.
- ↑ 1.0 1.1 Jones, Arwel Wyn Jones (2013-12-10). "Yay! Molly.".
- ↑ 2.0 2.1 Moffat, Steven (writer) & McGuigan, Paul (director). (25 July, 2010). "A Study in Pink". Sherlock (2010). Series 1. Episode 1. BBC One.
- ↑ Thompson, Steve (writer) & Lyn, Euros (director). (1 August, 2010). "The Blind Banker". Sherlock (2010). Series 1. Episode 2. BBC One.
- ↑ 4.0 4.1 4.2 4.3 Gatiss, Mark (writer) & McGuigan, Paul (director). (8 August, 2010). "The Great Game". Sherlock (2010). Series 1. Episode 3. BBC One.
- ↑ 5.0 5.1 Moffat, Steven (writer) & McGuigan, Paul (director). (1 January, 2012). "A Scandal in Belgravia". Sherlock (2010). Series 2. Episode 1. BBC One.
- ↑ 6.0 6.1 6.2 6.3 Thompson, Steve (writer) & Haynes, Toby (director). (15 January, 2012). "The Reichenbach Fall". Sherlock (2010). Series 2. Episode 3. BBC One.
- ↑ 7.0 7.1 7.2 Gatiss, Mark (writer) & Lovering, Jeremy (director). (1 January, 2014). "The Empty Hearse". Sherlock (2010). Series 3. Episode 1. BBC One.
- ↑ 8.0 8.1 8.2 8.3 Thompson, Steve; Moffat, Steven; Gatiss, Mark (writers) & McCarthy, Colm (director). (5 January, 2014). "The Sign of Three". Sherlock (2010). Series 3. Episode 2. BBC One.
- ↑ 9.0 9.1 9.2 9.3 9.4 Moffat, Steven (writer) & Hurran, Nick (director). (12 January, 2014). "His Last Vow". Sherlock (2010). Series 3. Episode 3. BBC One.
- ↑ 10.0 10.1 http://www.radiotimes.com/news/2017-01-17/sherlock-star-louise-brealey-disagrees-with-steven-moffats-comments-on-molly-hooper
- ↑ 11.0 11.1 http://www.springfieldspringfield.co.uk/view_episode_scripts.php?tv-show=sherlock&episode=s04e03
- ↑ Sherlock showrunner Steven Moffat: 'Molly broke our first rule', Mayer Nissim, Digital Spy, 9 December, 2013.