When Stan's father passes away, Stan reveals his real father is actually Jack Smith, a super suave spy. Jack convinces Stan to quit the CIA and work with him at the Scarlet Alliance, an ultra-secret spy group. Francine is upset with Stan, who is busy training with Jack for a mission involving uranium, artwork and terrorists. But when the FBI shows up at the Smiths' house looking for an international jewel thief, Francine suspects Jack is the fake.

When Steve's new relationship with his girlfriend gives Francine empty nest syndrome, she tries to convince Stan to have another baby. Meanwhile, Roger tries to enroll in college with Haley in order to experience college life, but while Roger ends up teaching the class, Haley finds a new crush in her classmate Ethan (Elijah Woods), who turns out to be far from normal.

After Stan is prosecuted for sending contaminated cattle to a slaughterhouse, he says that it began as a quest to make a man out of Steve. Meanwhile, Roger sparks a cat fight between Francine and Hayley, for reasons of his own.

While playing poker with the guys, Stan is found to be a virgin. Not in the traditional way, but in that he's never killed anyone. Roger and the guys help Stan bust his killing cherry.

Stan goes in search of a former KGB agent, Sergei, and is shocked to find that the man is his new next-door neighbor and that Sergei has already turned Steve into a communist. Meanwhile, Roger and Klaus head to France for a little R&R but their trip takes a turn for the worse when Klaus gets busted for drug smuggling.

Steve signs Stan up for a father-son bike tournament, but the plan veers off-track when Stan admits that his father never taught him how to ride a bike. Determined to make things better, Steve helps reconcile Stan with his convict father. Meanwhile, Hayley needs internship credit for school, so Roger hires her to bartend at his makeshift bar in the attic.

Steve joins a junior football team to make Stan proud. However, when a hyper-competitive Stan assumes the position of head coach, Steve gets kicked off the team for not being good enough. Out for revenge, Steve and Roger recruit a new team of misfits who threaten Stan's perfect season. Meanwhile, Francine and Hayley compete for a blue ribbon at the Langley County Fair.

Steve goes to work with Stan and discovers the N.S.A.. Hayley decides to let go of being a vegetarian and eat meat for one day.

A mold of Francine's vagina is displayed in a museum.