At the Clam, Cleveland reminds the guys that Father's Day is coming up and Peter wants to know why they haven't met Joe's dad yet. Joe admits they are estranged and Peter talks the rest of the guys into tracking him down. They try to surprise Joe with the news the day before his dad is due to arrive but Peter gives it away. An upset Joe informs them that the reason they are estranged is that his father Bud has made fun of handicapped people all his life and Joe had kept his a secret. Joe tries to get them to call off the visit but he is already on the way. Peter suggests hiding Joe's handicap. Peter tries to place a horse under Joe which fails when the horse runs amok when he tries to make it move by slapping it's privates with a damp towel. Cleveland makes a suggestion that Peter and Joe try to switch clothes and lives for the duration of Bud's visit. When he arrives, Bud and Peter get along well while Joe puzzles the Griffin family over his appearance in the house.
Peter bring Bud back from a ride along in the police car and they poke fun at Joe for being handicapped. When Bud is due to leave, Peter informs Joe that he invited him to move in with him and Bonnie. Joe and the Griffins try to talk sense into Peter who says he's happy to finally have a dad who is close to him and refuses to give it up. Hanging out with Bud, they observe Joe taking out the trash and Peter is sent over to tell him to stay inside. They dispute turns into a fight and Joe beats Peter up. Joe reveals that he is the real Joe and gets his dad to admit his anger stems from being afraid that he or someone in the family would become handicapped themselves and they all apologize. Later, Peter admits missing a pair of pants which are still on the horse which attracts attention from Mayor West.
Meanwhile, Lois takes Stewie to the doctor who informs them that Stewie will be very short as an adult. Brian takes Stewie to the mall to buy new clothes and he bumps into Tom Cruise while they both reach for the same shirt. Amazed that they are both the same size, he get invited to hang out with him for the day. They hit it off and Stewie tells Brian about spending the day with Tom. However, Lois gets a call from Dr. Hartman that he misread the chart and Stewie will be normal height. When Tom arrives, Stewie cuts off their relationship, angering Tom. At daycare, Tom suddenly appears during play time and frightens Stewie who runs home to Brian. He explains what is going on to a doubtful Brian. Setting up a trap in the park, they manage to trap Tom and send him off to Zappos, a clothing retailer, where the clerk greets him on his return.