First episode: A Study in Pink
Seen also in: The Blind Banker, The Great Game, A Scandal in Belgravia, The Reichenbach Fall, The Empty Hearse, The Sign of Three, His Last Vow
Occupation: Specialist registrar at St. Bart's Hospital
Show history: She is first introduced as the shy pathologist who has a crush on Sherlock. Her infatuation is used as a running joke throughout Season 1, as Sherlock uses it to his advantage to manipulate her into giving him access to the morgue ("The Blind Banker"). However, Molly unwittingly ends up being the tie between Sherlock and Moriarty when Moriarty disguises himself as her boyfriend in "The Great Game."
Season 2 shows Molly gradually becoming a part of Sherlock's small circle of friends, as the infamous Christmas scene in "A Scandal in Belgravia" shows as Sherlock, after humiliating her for the umpteenth time, actually takes her feelings into account and apologizes. "The Reichenbach Fall," though, is when Molly truly comes into her own, with this unforgettable scene between her and Sherlock in the lab:
Molly: You're a bit like my dad. He's dead. No, sorry-
Sherlock: Molly, don't feel the need to make conversation. It's really not your area.
Molly: When he was dying, he was always cheerful, he was lovely. Except when he thought nobody could see. I saw him once. He looked sad.
Molly: You look sad, when you think he can't see you. (nods at John) ...Are you okay? Don't just say you are, because I know what that means, looking sad when you think no one can see you.
Sherlock: You can see me.
Molly: I don't count.
Sherlock: [startled silence]
Molly: What I mean to say is, if there's anything you need, anything at all, you can have me. No, I don't mean- I mean- If there's anything you need- It's fine.
Sherlock: But-but what could I need from you?
Molly: Nothing. I don't know.
By deducing Sherlock and seeing him more clearly than he could even see himself, Molly becomes the trusted friend and ally Sherlock needs to pull off his greatest deception of all - his own death. In "The Empty Hearse," it is revealed that Molly played a key part in faking his death, and to thank her, Sherlock asks her to solve crimes with him for a day. She is present at John and Mary's wedding with her then-fiance, Tom, and in "His Last Vow" we are left with the news of Molly's broken engagement and a ticked-off Molly who slaps Sherlock three times across the face after he relapses into drugs.
The Empty Hearse - Molly and Sherlock share a SMOKING HOT kiss in Anderson's theory of how Sherlock faked his death
His Last Vow - Molly appears in Sherlock's mind palace, trying to save him from his bullet wound
My take on her: See Molly Hooper is The Woman and/or 5 Reasons Why Molly Hooper is Sherlock's Best Character
Basically, Molly has transformed from a shy, infatuated young woman to a complete and total badass, and I love her. I'm both very much looking forward to seeing more of her in Season 4, and worried that Moffat will somehow find a way to mess up her character to align with his definition of a "strong woman" instead of the quiet strength that she so awesomely exemplifies. I'm also not sure what to think of a potential Sherlock and Molly relationship; while Season 3 seemed to be planting the seeds for a deeper relationship between them, I'm not sure what it would entail for Molly. Will she end up being kidnapped and/or killed by Moriarty, now that she obviously means something to Sherlock? Will Moffat bring Irene back (as, I think, he inevitably will, given that The Sign of Three cameo) and make it some kind of awkward, terrible love triangle? There's as much potential for things to go wrong as there is for things to go right. I just really hope the writers continue to do Molly justice - she is one of the most relatable, real women on television, and she has the potential to pave the way for other ordinary, yet totally kickass female characters in television, both present and future.