Greg Focker (Ben Stiller) and his wife Pam (Teri Polo) are having a typical busy morning getting their two kids ready to go to school. At work Greg gets a visit from Andi Garcia (Jessica Alba), a former nurse, now working with a company that makes a male enhancement drug called Sustengo. Andi tries to convince Greg to become the spokesperson of the drug by telling him he will have a higher salary. Greg says he will think about it and takes Andi's card.
Meanwhile Jack Byrnes (Robert De Niro) and his wife, Dina Byrnes (Blythe Danner), talk about how Dr. Bob, their former son-in-law, cheated on their daughter. Dina is going to visit their daughter and is leaving Jack by himself.
Jack suffers a minor heart attack but manages to call 911 and he survives.
Back at the Focker household, the family is in the middle of dinner when Jack calls Greg informing him of his heart attack and appointing him as the new head of the family, the "Godfocker". Jack also tells Greg not to tell anyone since he wants to keep it a secret from his wife and daughter. As soon as he hangs up Greg feels empowered and asks Pam to set up a tour for The Early Human School, a private school they were considering sending their children to.
Two weeks later Jack and Dina visit them. During dinner, as Greg is carving the turkey, his son's pet lizard startles him, causing him to cut his finger splattering blood all over his guests. Soon after, Kevin (Owen Wilson) shows up heartbroken after having been dumped by his girlfriend. Pam offers him a place to stay but he and Greg assure her he's fine sleeping at the shelter where he volunteers.
The next day, Pam wakes up sick so she asks Jack to go with Greg to the tour at the Early Human School. There they mistake Jack and Greg for a homosexual couple.
Greg decides to take Andis proposal to be the spokesperson for Sustengo. He agrees to give a speech about it at a hotel. Greg tells Pam about it and asks her not to tell her dad. Their daughter overhears and tells Jack daddy is meeting up at a hotel with Andi, the person who gives daddy his boners. Jack is alarmed thinking Greg is having an affair with Andi.
That night Jack follows Greg while on his way to the hotel. At the metro, Greg confronts him asking Jack if he is following him. Jack says he is getting some organic milk and is forced to get off a few stops before Greg. At the hotel, the presentation goes great and Greg is congratulated by many. Greg and Andi are photographed together. When Jack returns home from following Greg, he finds Sustengo samples in a bag and decides to take one. When Greg comes home he finds Jack sitting on the couch waiting for him. Greg notices Jack has a boner and asks him if he took a Sustengo. Jack says he did and that he has had the boner for over 4 hours. Greg is alarmed and tells Jack he must get an adrenaline shot as soon as possible. Jack asks Greg to do it at home as he refuses to go to the emergency room in that state. As Greg gives jack the adrenaline shot, his son walks in and screams at the sight.
Jack googles Andi Garcia and finds a picture of her and Greg on her webpage. Jack is sure they are having an affair.
Greg had been planning to throw the twins a birthday party in the backyard of a new house he was building, but his contractor had dug a giant hole in it so having the party there was impossible. Kevin suggests having the party at his house since it is much bigger.
Greg, Pam, Jack, and Dina take the twins for an evaluation at the Early Human School. The girl does well, but the boy does not. Jack suggests the girl takes after Pam and the boy takes after Greg. The boy falls off the rock wall after having asked Greg for permission. They take him to the hospital since he has broken his arm. There Jack tells Pam she should divorce Greg and marry Kevin. Greg and Jack argue loudly and as he leaves, Greg tells Dina about Jacks heart attack.
Greg decides not to go home and goes to the house he is currently building. While he is there Andi shows up with Chinese food and drinks. Andi gets drunk and forcefully kisses and hugs Greg, but Greg resists and asks her to leave. Jack has come by to apologize but when he sees Andi and Greg embracing he leaves convinced that they are having an affair. Andi throws Gregs phone in the pit in the backyard and as Greg is down there trying to get it she dives in causing them both to pass out.
The next day, the twins birthday party is being hosted at Kevin's house. Greg shows up and the family is reunited. When he tries to apologize to Jack for arguing with him the night before, Jack punches Greg and the two start fighting. As they are fighting Greg tells Jack nothing happened between him and Andi. The two get distracted when Mr. Jinx, Jack's cat, begins to eat Greg's son's lizard. Jack begins to have a heart attack but Greg aids him and the ambulance soon comes. As he is getting into the ambulance, Jack tells Greg he believes him and that he is now the "Gregfocker".
Greg, Pam, Pam's parents, and Greg's parents are sitting together talking and getting along, but when Greg's parents mention they are planning on moving down the block, Pam's parents also decide to move so Greg and Pam start freaking out.