Watson is having lunch with Elaina March, the reputed head of a drug cartel. They banter until Watson gets a text. It's from Captain Gregson. The lunch was a set-up, an excuse to occupy March, so they can nab her bookkeeper. They arrest March.
Marcus asks Watson to come to the safe house because the witness, Karen Lloyd, is nervous. As she leaves the apartment, she runs into Andrew Martell who is pet sitting. Watson gives him her card.
She meets with the witness and calms her down. Karen and a police officer get in the elevator, but when it arrives on the ground floor, both are dead. The elevator never stopped or slowed down.
Two months later, they still don't know who or how the killer got in and out of the elevator. Captain Gregson and Watson meet with Elaina March and her lawyers who accuse Watson of harassment. They have pictures of Watson outside the school March's children attend.
Captain Gregson says they did that to show her that they could get to her anytime they wanted. Watson meets Andrew for lunch. Noticing a young woman on a cell phone in a no service area, Watson confronts her.
The police receive an anonymous tip to look into John Mason. Watson is suspicious. The tipster's name rings a dim bell. Watson goes back to the brownstone. It seems abandoned. She heads to the bookshelves, when she hears a noise. It's Sherlock.
Watson is not happy to see him. It's clear that she's deeply hurt by the way he left. She's managed to build her own life without him and tells Sherlock that she doesn't need him.
Sherlock waits outside Captain Gregson office. He apologizes. Gregson says he can come back, provided Watson agrees.
Marcus and Watson question John Mason. He claims he used an alias because he was meeting an escort. They offer him a deal to turn on March. He thanks them and wishes them luck.
Watson heads uptown when she notices the same girl following her. She gets the drop and they fight. She recognizes her moves and meets Sherlock's new partner.
Sherlock apologizes and tells Watson that he was afraid and angry, which is why he left. Later, he realized that he was a mentor and could replicate the relationship he had with her, which is how Kitty ended up working with him.
He tells Watson that he can work with the NYPD again, if she approves. She doesn't.
Watson goes to the brownstone. Kitty and Sherlock have solved the case. Mason/Elspeth used a magnet to trigger four spent bullets he had placed in the elevator. No proof, but they do have fingerprints of the killer who murdered a security guard while stealing a magnet from Rutger's University.
Bell, Watson and Gregson interrogate Mason/Elspeth. He denies everything again. Elaina March invites Watson for lunch. She gives a tip. It was a former drug cartel member who committed the murder, but she doesn't know where he is. She alludes to the fact that she expected Watson to be in the elevator and killed in the attack too.
Sherlock brings Watson a housewarming gift. Offers to give a fresh perspective. She declines. She reviews the tape of Elspeth leaving and notices that his suitcases look significantly lighter leaving than going in.
Bell and Watson go to March's home. They tell her that they found the magnet. Mason/Elspeth entered the witness protection program and March is arrested again.
Watson goes to Sherlock's brownstone. He congratulates her, but she interrupts to tell him that she told Gregson it was okay if Sherlock and Kitty were consultants. However, she and Sherlock are not partners, but can use each other to brainstorm when stuck. She asks him why he came back to New York. He says it is where he belongs.