Bee Branch is a 15-year old trying to solve the mysterious disappearance of her mother. Her mother, Bernadette, and her father, a Microsoft wiz, Elgin, agree to give her whatever she wants for a perfect report card, and when she gets straight A's, she asks for a trip to Antarctica. Bernadette arranges something for her, but we quickly learn that Bernadette's life is already interesting enough as it is.
Bernadette doesn't get along well with the other parents at Bee's school. She is in feud with a lady who says she ran over her foot. Bernadette isn't the normal stay-at-home mom though. She's a famous architect and a winner of the MacArthur "Genius" Grant. She builds a home and sells it, but the buyer destroys it out of jealousy toward Bernadette. We also learn about Bernadette's four miscarriages before Bee.
We flash back to just before the present moment, Bernadette has disappeared. Elgin learns that his wife's assistant was a Russian criminal positioning themselves to steal the family's wealth. He has an affair at work with Soo-Lin. When Elgin tries to tell Bernadette, she goes to the bathroom and disappears. Bee gets sent to Choate, an elite boarding school.
While at school, Bee learns that her mom's friend, Audrey, helped her escape from Elgin's meeting, showing her the correspondence between Elgin and his mistress. Bernadette sent this correspondence to her daughter to explain that she is waiting to confront Elgin when the two travel to Antarctica.
When Bee gets kicked out of her charter school, she urges her father to take her as promised to Antarctica. They steal a boat and go south, and they run into Bernadette who is bemused that everyone thought she was dead—she'd been writing letters to Bee the whole time. When Bee returns home, she finds the missing letter that explains everything: Bernadette has just been enjoying the sights of Palmer Station. She ended up having too much fun and not wanting to come home. The case is solved.
