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Bee's the queen, honey, but she's got issues. A disappearing mom? Check. A dad with an affair and a lovechild? Check. The typical awkwardness of starting high school? We don't know much about chess, but we're pretty sure you'd call that checkmate.
There's no denying that Bee is a stellar young woman. She's incredibly smart, having not just been accepted to the prestigious Choate Academy, but also given the opportunity to skip a grade. She's caring and compassionate. Plus, she's the Jimi Hendrix of the flute. You should hear her rendition of "The Star-Spangled Banner."
In truth, Bee is lucky to be alive. She "was born with a heart defect which required a half-dozen surgeries," but thanks to the support of her parents and doctors, she managed a full recovery (1.289). As for Bee, she doesn't remember much of these early experiences, as "for two-thirds of [her] life [she's] been totally normal" (1.298). She can't relate to that sick kid she once was.
In fact, the only time Bee is able to reconnect with that young, helpless version of herself is at a big Christmas performance she goes to with the Youth Group.
Here's what she imagines in her head:
I was baby Jesus. Mom and Dad were Mary and Joseph. [...] I was surrounded by the surgeons and residents and nurses who helped me stay alive [...] and if it weren't for them I would be dead now. (4.224)
What's funny is that Bee isn't even religious. Instead, she's using religious imagery to understand things from her own life: her helplessness, the selfless care of the doctors who saved her, and, most importantly, the endless love she received from her parents. Heavy stuff, but it makes sense that it would be on her mind given everything that's happening in her life.
Although Bee feels that love from both of her parents, she clearly connects more with her mom than her dad. The feeling is mutual. Bernadette hates most things, but the one thing that never fails to brighten her day is her daughter. We watch as they sing Beatles songs together in a wonderful moment of mother-daughter bonding, and we watch as Bee tries to help her mother through her many issues.
So it's no wonder that Bee turns against her dad after Bernadette disappears. Not only is Bee reeling from the fact that her mom dropped off the face of the planet, but she's also finding out that her dad had an affair with his coworker. Oh yeah, and she's pregnant with his child. Surprise. That's when Bee makes the "executive decision" to "hate him" (6.48)
Bee ultimately realizes that she's being too hard on her dad. Not for the whole affair thing. He deserves all the grief he gets for that gem of a decision. But it's not true that he doesn't care about Bernadette. Their relationship is just complicated. Really complicated. Although they might not be the sitcom-perfect family Bee longs for, they're not as broken as she fears them to be.
Similarly, Choate doesn't turn out to be the Hogwarts-esque dreamland Bee hoped for. She would have a hard enough time getting along with the "snobby rich kids" there under normal circumstances, but with Bernadette's disappearance heavy on her mind, it's downright impossible (7.101). Bee ends up returning to Seattle with plans to go to high school there, a decision that is almost certainly for the best.
Then, of course, Bee finds her mother in Antarctica. That's a long story in and of itself, but our biggest takeaway is that it shows just how similar Bee and Bernadette are at their core. A hare-brained rescue mission to Antarctica is a total Bernadette move. No matter how you slice it, it's a huge weight off Bee's shoulders to have her beloved Bernie back in her life.
In a meta twist befitting a former Arrested Development writer, the real culmination of Bee's story is the very book we've been reading the whole time. Using the documents sent to her by Audrey, she compiled and narrated the whole sordid tale of Bernadette's freaky disappearance, creating Where'd You Go, Bernadette?. It's a crazy accomplishment for a ninth grader, but given everything we know about Bee, it's no surprise. We just can't wait for her sophomore effort.