Stan Smith uses his CIA skills to help 13-year-old son Steve win class president and the heart of the hottest girl in class, Lisa Silver. But when being class president makes Steve mad with power, Stan must jump in to save the day. Meanwhile, Roger, the alien Stan saved from Area 51, helps 18-year-old Hayley with her school paper. In return, she hooks him up with boatloads of junk food to curb his sweet tooth. Unfortunately, some Chocodiles send him over the edge and a sugar crash prohibits him from finishing one of her papers, forcing Hayley to pick up the pieces. And Klaus, the goldfish with the brain of a German guy, pines after mother Francine. Unfortunately for Klaus, the closest he'll ever get to a date with her is the spin cycle with her sports bra.

Hayley comes home from a Green Party rally with her hair dyed green, instigating a fight with Stan. While she's sleeping, Stan cuts her hair (for her own good, of course). After learning of what Stan did, a wigged Hayley defies her father yet again by moving into the van of her new boyfriend. When Stan cuts her off financially, she gets a job as a waitress in a strip club, which pushes Stan right off the edge. Meanwhile, Steve tries to pass Roger off as his disfigured sister in order to cop a feel with a female classmate.

When Stan enters an essay contest to have his personal hero, President Bush, come over for dinner, he is overcome with joy when the President arrives at his doorstep. However, not everyone in the Smith family shares Stan's excitement. Hayley tries to drill President Bush on the Iraq war, and Steve and Roger attempt to convince him that they've found Osama Bin Laden, but instead get him drunk. Stan tries to save the President from public humiliation, while Hayley revels in his fall from glory.

A James Bond spoof casts Stan as a 007-type agent assigned by B (Bullock) to infiltrate the set of a movie producer named TchochkieSchmear (Klaus), who's in cahoots with the diabolical villain Tearjerker (Roger). Their plan? To kill everyone in the world by making movies so sad, people will cry themselves to death.

Stan emcees a CIA telethon to raise funds for the agency's torture budget after Congress slashed it. But Roger is out to sabotage it because Stan stole the idea for it from him.

When Stan refuses to switch Klaus back into his original body, he steals Stan's body; Roger builds a gym in the attic.