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Luna starts off with Regan, the main character, waking up to find that her sister has come into her room and is flouncing around in pretty clothes. Maybe this would normally be an annoying but typical sisterly thing to do, but it turns out that Luna is Regan's brother, Liam. Liam is transgender and acts like a boy during the day but changes into girl clothes at night to be his true self, Luna. He longs to transition and present as female, but their stodgy father and judgmental classmates make it difficult for him to come out.
The next day Liam is back in boy gear again. He drives Regan to high school and she goes to Chemistry class. Regan is normally quite the loner—her only friends are Liam and his best friend, Aly—but in class, she's suddenly paired up with a cute new boy named Chris. No, this isn't going to be like Twilight at all—we'll burst your bubble right now and tell you that Chris is just a normal boy sans supernatural powers. He is totally hot and is even trying out for football, and he and Regan spend the whole class period flirting. They have great chemistry (pun fully intended).
Regan regularly babysits for a family called the Materas. To Regan they're the perfect family and she loves going over to their house and fantasizes about one day being adopted by them. At home, Liam has been suffering from depression and angst and feels as though he can no longer live a lie. He decides that he needs to start transitioning, and even though she's freaked out, Regan agrees to go shopping with him on a Saturday. At school though, Chris asks Regan if she'll go to a rave with him on Saturday night—so poor Regan has to blow off the only date she's ever been asked on in order to support Liam. What a bummer.
The shopping trip turns out to be kind of a disaster. They go to the mall, where a clerk at the Gap physically recoils from Luna and a bunch of thirteen-year-old kids heckle them, and then when they go home, they're grounded for lying. The next week, they decide to go to Taco Bell with Luna in girl clothes. At the Taco Bell, Regan runs into Chris but mistakenly makes him think that she's there with a date; when she gets to school later, she finds out that he's dropped Chemistry class. Things are turning out pretty bleak for her love life.
Luna is getting more and more intent on transitioning and even meets a transgender girl on the Internet named Teri Lynn. Their dad confronts Regan one day and asks if Liam is gay, but she says no. Aly also confront Regan and wants to know whether or not Liam is going to ask her to prom. Regan runs into Chris, who asks her out to a party on Friday night. Even though she has babysitting to do, she says yes. She and Liam hatch a plan to get her on the date—he'll sneak in after she leaves for the party and watch the kids while she's out.
The date totally does not go as planned and is a disaster from the start. She and Chris get into all sorts of trouble, including forgetting her purse, getting a speeding ticket, and getting her back late. When he drops her off, the Matera parents are already home and are panicking because they've caught Liam dressing up in Elise Matera's negligee, jewelry, and makeup. They kick both of the siblings out and tell Regan that she's not allowed back in their home. When Liam spends the whole night crying, she doesn't go to him.
After all the shenanigans, the siblings eventually make up and Liam reveals to Regan that Teri Lynn is going to come into town and he's going to meet up with her. He also decides that he's going to come out to Aly. When Aly is over one afternoon, he tells her that he's transgender, but she doesn't take it well. Super bummer.
At school, Regan receives a note from Chris telling her to meet him in the gym, and when she gets there he reveals that he went back to the party to get her purse and that he's still totally interested in her. Regan is in the process of telling him that she totally digs him too when she notices a disturbance—Hoyt (a school bully) is picking on Liam, who has appeared at school as Luna. Regan freezes up because she's so horrified that Luna has revealed herself at school. Instead of going over to help her sibling though, she runs away.
That night Luna comes into Regan's room and tells her that it's okay that she ran away; she doesn't care about it at all. Luna goes to meet with Teri Lynn and is thrilled. The next day at breakfast, Luna comes down dressed as… herself. Predictably, their dad completely freaks out while their mom just ignores the scene unfolding before her. Later on, Aly comes over and says that she wants to play video games with Luna.
Regan goes on a date with Chris where she seems distracted and off, since her mind is (understandably) on family stuff going on. Instead of getting annoyed, he asks her out for the next week. Back at home Regan is woken up in the middle of the night by Luna, who tells her to get in the car. As they drive, Regan realizes that they're headed toward the airport, and that Luna is leaving for Seattle to stay with Teri Lynn. Even though Regan is sad that Luna is leaving, she realizes that for her sister to flourish, she needs to live her own life. They both do.