When Principal Shepard is suspended from James Woods High after a mental breakdown due to his ugly divorce, Peter volunteers to take his place as interim Principal.
The Griffins go to a waterpark for Lois and Peter's anniversary (his idea), where Chris meets a girl named Isabella and decides to ask her out. She wants to say yes, but she informs Chris that she has two young children.
Peter and Lois receive a note from Principal Shepherd pinned to Chris' backpack. During their meeting they learn that if Chris doesn't pass his upcoming history exam he will have to repeat the 9th grade.
Meg is worried that she won't do well on her SATs, so she convinces Brian to take the test for her. A confident Brian agrees to the challenge, and even dresses up like Meg, only to find out that he received the lowest score in the class.
At Stewie's graduation, Brian states that Stewie's proud moment is no big feat. Stewie takes it upon himself to try and acquire some real world knowledge. Meg is discovered by a photographer who asks her if she would like to model for him.
After some convincing from Peter, Jillian gives Brian an ultimatum that the two of them need to move in together. He reluctantly agrees but is embarrassed because he can't afford the rent. In turn, Brian decides to take on a roommate, Stewie.
Brian surprises Lois for her birthday with two tickets for a cruise. After Peter and Lois embark without their baby Stewie, he takes revenge by pulling off his life-long dream of killing his mother.
After Stewie shot his mother in cold blood on the deck of the cruise ship, Lois returned to Quahog, entering the courtroom just before Peter was sentenced to life in prison. Stewie escapes the courtroom and along with his hostage Brian, he moves forward with his diabolical plans to take over the world. The only person in the world who can stop him is his mother, Lois.
Peter finds out that his mother gave birth to him in Mexico years ago and because she never got him a U.S. birth certificate, it turns out that he is an illegal immigrant. Peter is let go from his job at the brewery and because of his lack of citizenship, cannot find any work. Lois's father Carter steps in and helps the family, giving Peter a job working on his property. Peter learns the difficulties of being an illegal immigrant living in the United States.
Quahog is experiencing a flash flood, and the Griffins house is filling with water. Before the family can escape, Meg gets trapped in the kitchen, and is found unconscious. She is rushed to the hospital, where Peter vows to never let anything happen to his little girl again. When Meg awakes, she falls for her young intern doctor, Michael, and the two start to date against Peter's wishes.
After his presidential limo breaks down in front of the Griffins' house, Bill Clinton and Peter become good friends.
The Griffin family comes into some money after finding a rare coin under their carpet. They decide to use this windfall to open a restaurant in Quahog. When business doesn't seem to be booming, Joe comes to the rescue by promising to make it the new local hangout for him and his friends. Peter assumes Joe's friends would be his cop buddies, but instead it's his disabled friends that arrive, much to Peter's chagrin.
When Stewie vomits after chugging wine from the chalice in Sunday morning church, the Griffins are run out of Quahog by an angry mob of townspeople who fear that Stewie is possessed by the devil. The family escapes to Lois' sister's house in Texas where they each try to adapt to their new environment.
The Griffins vacation to the mountains of Quahog and discover that a local oil refinery is polluting the lake. After all of their hair falls out from swimming in the body of water, Lois decides to take action by running for mayor.