Frasier is nervous about having sex with Julia. Roz hates her new job after only one day and decides to come back to KACL and pretend she had never quit. Niles admits to Daphne that when he was a student he had donated sperm to a sperm bank, but when he checks on what happened to it he discovers that it was discarded due to low motility.
Niles convinces Frasier that the reason he has no luck with women is that he gets hung up on little faults. When he tries to be more tolerant of Julia, however, she proves to be obnoxious during a party at Frasier's apartment, and she ruins Niles and Daphne's plans to break the news of Daphne's pregnancy by blurting it out during dinner.
Frasier suspects Roz's new boyfriend Barry of being gay and mistakenly thinks he goes to a gay bar. When Frasier visits the bar trying to find Barry, he is recognized by people in the bar and soon all of Seattle thinks he is gay.
Meanwhile, Frasier tries to build a friendship with Alistair Burke, a famous opera producer. Burke turns out to be gay and thinks Frasier wants a sexual relationship with him.
Roz tries to set Frasier up with her friend Ann, since Roz is concerned that Frasier is getting out of pratice with dating women. Although Frasier isn't interested in Ann, he agrees to take her to dinner. However, Kenny is also taking Liz Wright, who has a job offer at a Seattle art museum, out to dinner in the same restaurant. Kenny tries to get Frasier to agree to give Liz a tour of Seattle to persuade her to take the job. Since Liz is stunningly good-looking and Ann turns out to be a bore, Frasier tries to dump Ann so he can join Kenny and Liz at their table.
Frasier's first day back in private practice goes from bad to worse as he embarrasses himself with every patient who comes to see him.
Meanwhile, Maris phones Niles desperate for help in dealing with an abusive Argentinian boyfriend. Niles agrees to meet Maris for lunch, and is about to tell Daphne when he changes his story and claims he was out planning a surprise baby shower for her. At the shower, Maris's boyfriend shows up and punches Frasier. Later, there is a news report that Maris has been arrested for her boyfriend's murder.
After Maris's arrest for murder, the press learns that Niles had given her the antique crossbow that was used as the murder weapon. Niles and Daphne's lives become hell when they are hounded by the press, and although Niles appears to be coping well, he eventually disintegrates in public by taking all his clothes off at Café Nervosa.
Niles is basking in the fame and public attention he is getting from his connection to Maris's murder case, making Frasier jealous. When Frasier learns he has been nominated for two awards at the Seattle Broadcasters (Seabees) gala, he tries to make the most of his situation to put Niles in his place, but things don't go as planned.
To raise money for charity, the KACL staff challenge the staff at KPXY to see who can lose the most weight in two weeks. The contest becomes personal when Frasier discovers that the station manager at KPXY is a guy who used to bully him in school. Meanwhile, Niles and Martin try to nurse back to health a pigeon that flew into a window in Frasier's apartment.
When Frasier discovers that Martin never mailed in the insurance renewal for his apartment, he is in a panic to get new insurance. Roz suggests that Frasier make amends with Ann (from episode 11x05 - The Placeholder
) by buying the insurance from her. Ann reluctantly agrees to assess Frasier's apartment but while there, slips in Frasier's kitchen and breaks her leg. Worried that Ann will sue him, Frasier suggests that she stay with him until she gets used to her crutches. However, Ann is convinced that Frasier is in love with her, and refuses to leave.
Meanwhile, Niles and Daphne try to retrieve an embarrassing painting from Maris's house.
Frasier gets annoyed when Martin constantly sneaks up behind him and scares him. Since he has a clown suit for use in therapy in dealing with one of his patients who has a fear of clowns, he decides to get his revenge on Martin by dressing up in the clown suit and pretending to attack Martin with a meat cleaver. Unfortunately, he scares Martin so much that he has a mild heart attack and ends up in hospital. While he is recovering, Martin asks Ronnee to marry him.
Frasier is getting disillusioned with the way his life is going as his job is becoming dull and he is still unable to get into a meaningful relationship. So when his elderly neighbour Opal asks Frasier for help changing a lightbulb, he decides to do something risky and impulsive, and steals a medal that Opal won at the 1936 Olympic games. Afterwards, overcome with guilt, he persuades Niles to help him return the medal to Opal's apartment in secret.
Frasier accidentally gets off the elevator on the wrong floor in his apartment building and meets Charlotte, who runs a matchmaking service. She convinces him to sign on with her, even though her fee is $10,000. After a series of disastrous dates arranged by Charlotte, Frasier discovers that Charlotte herself is having problems in her own life, and starts to have feelings for her.
Niles and Daphne are considering having a natural birth for their child.
In part 1 of the finale of Frasier, Frasier struggles to put together a wedding for Martin and Ronee, Some of Daphne's brothers come to Seattle and Frasier gets an offer from his agent that he is considering whether to take or not.
In part 2 of the finale of Frasier, Eddie is taken to the vet by the family during Martin and Ronee's wedding rehersals, Niles and Daphne have very good news. Martin prepares to move out of appartment 1901 and Frasier decides on the offer put to him by his agent.