It's the end of summer vacation and things are starting to get tense for Ellen, her math prodigy of an older brother, Link, and Link's best friend, James. For a while now they've been an inseparable trio, but now they're also developing into an unfortunate love triangle: Ellen is madly in love with James, but James is in love with Link. And Link, poor Link, just doesn't know how he feels about that.
Ellen starts at her new school and she's filled with anxiety. She prefers to fly under the radar socially and academically, but at Cedar Hill everyone knows she's Link's little sister. She's determined to have a fresh start and be more social (no more teacher's notes on her unwillingness to make friends), but that proves to be difficult for her. (Hey teachers, there's nothing wrong with being introverted.)
One day at lunch, a friend observing Link and James remarks upon how much they seem like a couple, and the remark effectively blows Ellen's mind—of course they're a couple. So now she's consumed with the need to define their relationship in order to better understand her two favorite people.
Her first step is to ask her mom. Mom says that she wants Link to do whatever makes him happy (typical Mom thing to say) and that if Ellen really wants to know, she needs to ask him.
This advice turns out catastrophically. Ellen finally screws up enough courage to ask the boys if they're a couple, and things explode. James says yes, they are, but Link adamantly denies being gay, despite knowing that James is. Link storms out, and Ellen and James are left to sift through the remains of the fight for little kernels of truth.
Ellen decides that she needs to educate herself about what it means to be gay, but no matter how many books she reads, she can't seem to find the answers she wants.
Link starts dating a girl, so James and Ellen turn to each other for companionship. They start frequenting hospital cafeterias and playing games that teach them how to really "see" people. He starts teaching her how to draw, and over time their companionship turns into something more, and they start dating each other.
Poo really hits the fan when the school calls their parents to report that Link left all of his final exams blank. That's one heck of a cry for attention, and oh boy does he get some. His mom insists he see a shrink to talk about whatever it is that he's going through. His Dad just wants his academic super-star to keep on shinin', though, so he wants him to take his exams over, see the shrink for performance anxiety, and for Pete's sake, keep quiet about the fact that he's been paying him to date a girl. Say what?
Link finally agrees to see a shrink who specializes in math geniuses, but he holds firm on refusing to retake his exams. He also comes clean about his secret piano lessons, which surprises everyone. Ellen just continues to love James and wish she understood her brother at all.
Things also remain tense in the McConnell house: Link resumes his hostile interactions with anyone who loves him; Dad maintains his impressive state of denial about Link's possible homosexuality; Mom keeps pretty neutral; and Ellen spends most of her days obsessing about James, sex, homosexuality, her lack of sex, the possibility of sex, and James (oh, did we say that one already?).
Then: Link reveals to his parents that he got into Yale. For his Dad, it is a dream come true—the Holy Grail of possible educational institutions. Somehow this manages to diffuse their overwrought situation, and they all go out to celebrate.
James confesses to Ellen that he's going to Art School in Germany. She's heartbroken, because that distance is practically insurmountable for a fourteen year-old. As consolation, they finally have sex.
As Ellen blissfully walks home from James's house after the loss of her virginity, she envisions a bright future for herself.