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As Liam's best friend, Aly should be the one person that he can rely on with his secret, but he actually doesn't tell her until later. The problem is that even though Aly's known Liam for so long and knows his tendencies, she doesn't want to believe that he's transgender or even gay. She has a crush on Liam and would rather believe a lie than face the truth:
She opened her mouth, and shut it. Shaking her head at the skylight, she said, "But I'm not the same. What does this make me? A lesbian? I don't think so." She broke away from me and stalked off. (23.76)
Aly doesn't want to accept that Liam is transgender because it affects her own life; she's not prejudiced, she just wants Liam to love her back and to have a heterosexual relationship with him. When she realizes that this can never happen, she starts to come around and accept Luna:
"I don't know how long it's going to take me to be okay with this." She spoke to the empty space between us. "It's hard. You know?" (25.23)
Even though it's hard, Aly's willing to work through it and accept Luna. Because after all, that's what friends do.