After Charlie's night with a girl is ruined due to Alan's interruption, Alan moves in, being kicked out of his house by his "suffocated" wife: Judith. The next day Alan brings over his son, Jake while he and Judith can talk about their marriage. While eating, Alan finds out that Judith is a lesbian therefore their relationship ends. Charlie takes to Jake, and begins to take him shopping to meet girls and lets him play at his poker games. Upset, Alan moves in with their mother, Evelyn, taking Jake with him. Charlie now feels surprisingly empty and invites Alan and Jake to move back in, convincing Alan that all their problems in life are because of their controlling mother and that Jake would only end up being just as messed up in later life.

While spending time with Jake, Charlie finds it hard to enforce rules that Alan has set out for him. It gets to the point were Jake lures a flock of sea gulls into his room, and Charlie gets very upset. This prompts Jake to try and get Charlie to forgive him. Alan starts doing chores for Judith, in the hopes of them getting back together. During one of the tasks, Judith kisses Alan, leading him to believe that things will get back to the way they once were.

After spending a day at Disneyland, Jake gets sick and wants to go to his mothers' house, to have her take care of him. This sends Alan into a state of misery, as he realizes he's losing his wife, and son. Charlie suggests that they go drinking, and Alan agrees. After drinking the boys take a cab home, but at one point they end up at their mothers, where they try to tell her what they think of her, but fail in getting the point across.

Charlie is very unhappy with his housekeepers' decision to quit, after she experiences Alan's demanding ways. Alan then offers to take on the role of housekeeper, but this situation doesn't work at all. So Alan decides to get the housekeeper to come back. Before Alan leaves, he puts Charlie in charge of getting Jake ready for a dinner with his mother and grandparents. Charlie also tries to get Rose to move on, and date other men. He finds both situations to be bigger challenges then he first thought.

After spending a 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 sets up a play-date with an unattached mother named Kate, and they hit it off. During one of their dates, Charlie seems like he's ready for a serious relation. 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, and he has no idea. During the evening another soccer mom, Brooke, tries to move in on Gloria's plans.

Charlie tries to teach Jake to avoid certain calls that Charlie doesn't want to deal with, like his mother (Evelyn) for one. Evelyn gets so frustrated with not being able to talk to Charlie, that she decides to drop in while in the neighborhood. She invites them to dinner, to meet her new boyfriend (Tommy). When the brothers get over to their mothers house, Charlie is shocked to realize that Tommy's daughter is Olivia, one of the people he has been avoiding. Olivia tries to confront Charlie about their situation, but doesn't get the answer she wants, and throws a drink in his face, then storms off. After a week of not being able to contact their mother, Alan gets worried about her. So the brothers decide to go to her house and see if she's okay. They find her sitting in the dark and drinking, and she informs them that Tommy dumped her for a younger women. Later the brothers get Jake to try and cheer her up.

Judith gets worried when, for a school assignment, Jake draws the tattooed buttocks of a female surfer friend of Charlie's who is in the habit of walking around his place half naked. Then Alan gets worried about Judith after she becomes friends with the surfer girl.

Alan tricks Charlie into joining him and Judith in leading Jake and his classmates in the school's annual music show.

After meeting Wendy, a one-night stand of Charlies, Jake befriends her. Charlie doesn't like this situation, as he believes Wendy is using Jake to further their relationship, and he has no intention to keep it going. It gets to the point were Wendy even starts spending time with Evelyn, and Charlie becomes desperate to get rid of Wendy. After Charlie breaks it off Jake becomes very unhappy with him, because he won't be able to see Wendy anymore. This forces Charlie to confront Jake and explain the situation as best as he can. Rose sees that Alan knows how to play scrabble, and asks him to teach her to play, he agrees. During the scrabble games the two bond, and Charlie suspects that she is using Alan to get closer to him, but doesn't pursue the issue.

In an attempt to prove that he is a family man, Charlie invites Lisa over for Thanksgiving dinner

While at the movies, the brothers bump into Judith and her new boyfriend. Seeing that Judith has changed her look, and the fact that Jake doesn't think Alan is as cool as Judith; prompts Alan to realize that if he wants to get back into the dating scene, he's going to have to change his look as well.

When Berta is forced to bring her granddaughter Prudence to work with her, the boys find themselves a little preoccupied with her.

Charlie finally gets a chance for a double date with a hot neighbor, who is out for revenge on her cheating husband, and her sister who's a hot soap opera actress, and needs Alan to come along. The problem is that Alan gets sick from 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.

Stan, Charlie's accountant, tries to explain Charlie's financial woes to him.

Against Alan's judgment, Charlie falls for a seemingly crazy woman named Frankie.

Frankie tells Charlie and Alan why she and her daughter are on the run; Frankie's daughter has a crush on Jake.

Alan offends Charlie by choosing harebrained cousins as Jake's guardians in the event of his death.

Charlie is stunned to learn his ex-girlfriend is now a man.

Judith's sister, Liz, hits on Alan at Jake's birthday party; Evelyn prefers alcohol to cake.

Judith believes that Jake is having a hard time dealing with his parent's divorce, after he starts annoying everyone with his non-stop guitar playing. So she suggests that they send Jake to a therapist. Alan doesn't agree at first, but after thinking about it, he believes it might not be such a bad idea.

Charlie jeopardizes Alan's divorce settlement by sleeping with his attorney, Laura.

Charlie attempts to cure Alan of his recent bout of sleepwalking; Jake sees his therapist.

Charlie tries to sweet talk Judith's divorcee support-group into letting Jake continue to spend weekends at his place.

A pregnancy scare has Charlie heading to the doctor for a vasectomy.