After 12 years of marriage, his wife Judith, kicks Alan out. He turns to his older brother Charlie for help. Charlie has trouble adjusting his carefree lifestyle with the presence of his 10 year old nephew.
Alan punishes Jake for an incident at Judith's house. Charlie is lax in enforcing Alan's restrictions, then some seagulls invade Charlie's house as a result of Jake's actions, Charlie has to learn how to discipline his nephew.
As Charlie tries to write a new jingle, Berta quits. Alan tries to convince her to come back. Leaving Charlie to get Jake ready for a dinner. And Rose tries to get Charlie's help to prepare for a date.
Jake sees a butterfly tattoo on the firm bottom of a surfer-chick friend of Charlie's and draws a picture of it for school. Of course, this enrages Judith until she becomes very good friends with the woman herself.
After being tricked into helping Alan and Judith produce Jake's classroom musical, Charlie is flattered to find out that the kids know all the words to his jingles. Alan is blind-sided with divorce papers from Judith, causing strife which results in Charlie, who refuses to deal with the pre-pubers without a snootful, having to produce the play on his own. Jake is crushed when he realizes that a reconciliation between his parents may never happen.
Thanksgiving winds up being the least thankful day of the year for Charlie, who has to bribe various members of his household to even come to a traditional turkey dinner. Not only are the usual feuds in evidence (leading to a turkey-carving right out of "Psycho") but Judith's parents are actually sympathetic to Alan and hostile to their own daughter for her "fling" with lesbianism.
Now Frankie has tricked the Harpers into taking her and her daughter Joanie in, she explains that Bob's parents want her declared mentally incompetent in order to get custody. Charlie wants to dump her, but Alan insists on taking them both in. Jake doesn't enjoy the 8 year old's 'romantic' attention. Charlie hates the consolation kisses and compliments, and is stunned when Frankie prefers intimacy with Alan. Charlie rightly warns him he's just falling for his 'damsel in distress', but warns her not to hurt his kid brother.
Jake plays electric guitar all day long and doesn't want to do anything else. Alan and Charlie can't figure out why. Jake refuses to discuss anything with anyone, including his grandmother and even a psychologist.
Charlie tries to seduce Alan's divorce lawyer, Laura, and her assistant. He sleeps with Laura and they decide not to tell Alan anything since it's unethical, considering that Charlie is a participant in the case.
Jake repeats something Charlie says to Judith. Then Judith refuses to let Alan take Jake for the weekend. Alan tries to talk to Judith, but encounters resistance from Judith and her friends. It's up to Charlie to set things right.
Charlie is sure he isn't ready for fatherhood after a year of trying to raise Jake, so he opts to have a vasectomy. But when the doctor performing the procedure keeps getting calls from his wife -- who's about to give birth -- Charlie starts to think about what fatherhood might entail and likes the idea, provided he still has his vital organs intact (in more ways than one).