Carefree bachelor Charlie Harper (Charlie Sheen)'s life is turned upside down when his brother Alan (Jon Cryer) and ten-year-old nephew Jake (Angus T. Jones) move in with him when Alan's wife Judith (Marin Hinkle) kicks him out after 12 years of marriage. After returning from a meal in which he failed to reconcile with his wife, Alan finds Charlie to be an irresponsible caretaker for Jake after Charlie allows him to play poker, so he takes Jake to move in with his mother, Evelyn (Holland Taylor) instead. But when Alan learns that Jake likes Charlie more, he decides to move back in with him and stay there. Meanwhile, one of Charlie's one-night stands, Rose (Melanie Lynskey), is stalking him. Alan lets her into the house thinking that she is Charlie's housekeeper and she glues all his cabinets shut.

When Jake starts feeding the seagulls after Charlie (who is afraid of seagulls) warns him not to, the gulls gather all over Jake's room, causing tension between Jake and Charlie. This gives Charlie an idea of what parenting can be like. Meanwhile, Alan tries to win Judith back by repeatedly going over to her house to fix things; after Alan snaps and tells her that he has had enough and that she is free, the two end up sharing a kiss, but Alan eventually tells Judith that the marriage is over.

Jake brings his pet guinea pig to Charlie's house. Jake becomes ill and wants to go back to his mother's, which upsets Alan. To make matters worse, the guinea pig suddenly dies, which Alan sees as symbolic of the way his life is falling apart. He gets depressed and has a drink with Charlie. After their drinking binge they confront their mother for the way they are, but chicken out. It is later revealed that their drunken cab journey home was taped and put on a TV show.

Charlie's housekeeper Berta (Conchata Ferrell) quits because Alan keeps criticizing her housekeeping skills. Alan is willing to take over her duties, but Charlie misses all the little things she did for him, like making his coffee taste "Christmassy". So Alan tries to make peace with Berta by finding her and attempting to bring her back. Meanwhile, Charlie tries to get Jake ready for his mother who is coming to pick him up – but Jake is more interested in fixing his bike's chain.

After spending a wild night in Las Vegas, Charlie decides to live up to his promise that he made to Jake about attending his soccer game. During the game, Charlie hits it off with an unattached soccer mom named Kate. Alan sets up a meeting with Gloria (one of the soccer moms) to write a soccer newsletter, but Gloria has other intentions for the evening, unrelated to soccer.

Charlie has dated the daughter of Evelyn's new boyfriend, and tries to avoid meeting her again. Evelyn's boyfriend discovers this and then dumps her, not because of what happened with Charlie and his daughter, but because Evelyn's boyfriend leaves her for another woman. This makes Evelyn depressed and she doesn't leave Charlie and Alan alone – spending hours performing songs in front of them and Jake in the living room. Charlie finally fixes this with a long and deep conversation.

Judith gets worried when Jake draws the tattooed buttocks of a female surfer friend of Charlie's, who walks around his place half naked. Charlie wants to sleep with her but she only visits his place to shower after surfing. Alan feels concern for Judith when she befriends the surfer girl. Jake begins to learn from Charlie about fake and real boobs and doesn't stop comparing them both.

Alan tricks Charlie into joining him and Judith in leading Jake and his classmates in the school's annual music show, which Charlie does not enjoy. Meanwhile, Alan discovers that Judith has filed for a divorce and is not happy. When he and Judith talk about the divorce, Charlie takes over the play; he soon enjoys the ride when the children learn he is the writer who wrote their favorite jingles. The children choose Charlie's songs instead of Alan and Judith's and confuse the parents attending the show, who'd thought that the show would have music sticking closer to traditional themes.

Charlie wants to dump a female friend that Jake has grown close to, while Alan and Rose bond over a game of Scrabble. It is revealed that Rose bonded with Alan to get closer to Charlie. Jake gets mad at Charlie for letting his girlfriend dump her.

In an attempt to prove that he is a family man, Charlie invites his ex-girlfriend, Lisa (Denise Richards), over for Thanksgiving dinner. He must also convince his family to join him as well, which also includes Judith and her parents. The atmosphere becomes awkward after Evelyn announces to Judith's parents that their daughter is gay; Judith becomes annoyed when her mother takes Alan's side in their divorce.

While at the movies, the brothers accidentally bump into Judith and her new boyfriend, who turns out to be Jake's soccer coach. Seeing that Judith has changed her look, and the fact that Jake doesn't think Alan is as cool as Judith, Alan realizes that if he wants to get back into the dating scene he's going to have to change his look as well, with Charlie's assistance. The new look earns him several compliments, but he gives up at the end, confessing Charlie that he is afraid of it.

When Berta has to bring her granddaughter, 16-year-old Prudence (Megan Fox), to work with her, the two men find themselves a little preoccupied with her, and Jake gets a big crush on her. Judith almost catches her walking around in a bikini, but Charlie and Alan manage to hide her. Prudence later shows up with her new fiancee asking to spend the night at Charlie's home before going to Las Vegas to get married, but Berta arrives and stops her.

Charlie finally gets a chance for a double date with a hot neighbor and her sister (who's a hot soap opera actress), and needs Alan to come along. The problem is that Alan catches an illness from a sick Jake, so Charlie takes them to a steam room to help Alan get rid of his flu symptoms. This backfires, as Charlie also gets sick, but he has no intentions of canceling the date, desperate to go to bed with her.

After Charlie's credit card gets declined, he decides to visit his accountant. The accountant, Stan (Richard Lewis), tries to explain Charlie's financial woes to him: Charlie spends faster than his royalty checks come in. Alan coaches Charlie on how to live frugally. Alan then suggests that Charlie could borrow money from their mother, but Charlie gets annoyed when Evelyn asks to take them out for lunch, and he refuses. Eventually, Rose lends the money to Charlie, and he promises to pay her back.

Against Alan's judgement, Charlie falls for a seemingly crazy woman named Frankie (Jenna Elfman) whom the brothers find smashing up a BMW in a parking lot with a baseball bat. She reveals that she has nowhere to stay, and Charlie invites her to spend the night at his place. The next day, Frankie says she needs to pick something up, which turns out to be her 8-year-old daughter.

Frankie tells Charlie and Alan why she and her daughter are on the run. Frankie's daughter has a crush on Jake, who doesn't respond to this. Frankie and Alan end up sharing a kiss, and Alan takes her and her daughter out for a picnic, with hopes of starting a relationship with Frankie. Frankie eventually says that she cannot date Alan, even though she does spend the night with him. As she leaves for Seattle, she gives him her bra as a memento of her.

Alan offends Charlie by choosing their cousins from Rhode Island as Jake's guardians in the event of his and Judith's deaths. After Alan goes out, Charlie accidentally injures Jake during a basketball game, but manages to take good care of him by driving him to the hospital. This makes Alan realize that Charlie can take care of Jake and he chooses Charlie to be Jake's guardian when he and Judith pass instead.

Charlie goes to meet his ex-girlfriend, Jill, who has invited him to the bar, but he is stunned when he learns that Jill is now a trans man (Chris O'Donnell) who calls himself Bill. Berta greatly enjoys the situation, especially when Evelyn meets Bill and they start dating.

Judith's sister Liz (Teri Hatcher), whom Charlie slept with at Alan's wedding, hits on now-free Alan at Jake's birthday party. In order to keep her sister separate from his ex-husband, Judith does claims she's going to seduce Charlie, a tactic which works successfully. Elsewhere, Evelyn prefers alcohol to cake and becomes inebriated during Jake's party.

Judith believes that Jake is having a hard time dealing with his parents' divorce, when he starts annoying everyone with his non-stop guitar playing (he only plays one song over and over). She suggests that they send Jake to a therapist (Jane Lynch). After the adults make many futile attempts to speak with him, Jake comes downstairs in a cheerful mood. When they question each other about it, Berta reveals that she spoke to Jake and gave him prune juice; he was constipated. The episode ends with a jam session of Charlie, Alan, and Jake, with Jake running off to the restroom thanks to the prune juice.

Charlie jeopardizes Alan's divorce settlement by sleeping with his attorney, Laura (Heather Locklear), who takes a liking to Charlie and blackmails him with Alan's settlement if he breaks up with her. After Charlie stupidly breaks up with her, Laura spitefully grants Judith with most of Alan's personal possessions. Though Alan fires Laura and has her decisions negated, he furiously chases Charlie around the house.

Charlie attempts to cure Alan of his recent bout of sleepwalking. Jake sees his therapist, who ends up treating Alan, too.

Judith has her support group over, and Jake repeats Charlie's negative comments about women, in which Charlie said that as long as you have a woman for sexual pleasure and another for cleaning, there should be no reason to get married. Furious, Judith prevents Jake from going to Charlie's the following weekend, until Charlie manages to woo her support group by having them, too, spend some time at his house.

A woman with whom Charlie has had sex thinks she is pregnant, but turns out not to be. Following this close call, Charlie attempts to get a vasectomy. At first he seems okay with the idea after witnessing how troublesome babies can be, but after seeing how happy his doctor, Dr. Sperlock (Terry Rhoads), is when he learns he is going to be a father, Charlie decides against the operation – and scores a date with the doctor's assistant.