JJ's secret

MASSIVE SPOILERS HERE!!

Throughout the game, there are references to JJ having a "secret". These are kept vague until the game's finale.

At the start of the game, JJ arrives on the Island of Memories with her friend, Emily. The two are seen talking to each other romantically, and it is implied they are lesbians. At one point, Emily reaches for JJ's hand, but JJ pulls away, before later leaning closer to Emily. Shortly after this, Emily goes missing and JJ must search for her.

Eventually, JJ receives a text message from her mom, who is cleaning the house while JJ is away at college. JJ tells her mom not to go into her room, but she does so anyway. JJ's mom finds clothes in the closet that seem suspicious to her, "a young girl's clothes". JJ claims they are Emily's clothes from when Emily was staying over. JJ's mom tries to return the clothes to Emily's mom on the way home from church, but Emily's mom points out that the clothes aren't the sort that Emily would wear, and that they're too big for her.

JJ's mom finds JJ's diary, and learns of JJ's secret. She asks JJ to see a counselor, to deal with the "abnormalities in your mind."

Later, JJ discovers a social media page from a Facebook-esque site that contains her pictures. A fake profile of her, with her nicknamed "Princess Packing Extra". JJ becomes upset over the idea that people who search for her will find this fake page, but Emily says not to worry about it, as the harassment will eventually stop when the bullies get bored and move on.

In the end of the game, when JJ is revived and wakes up from a suicide attempt as Post-Clear JJ, the secret is revealed: JJ is a transgender woman. Players can now play as Post-Clear JJ and experience the game with a brand new set of voice acting.

If players collect all of the donuts, they earn a special set of pictures that show Emily and Post-Clear JJ picking out female clothing.

Phone calls
At a few points in the game, JJ receives phone calls from Emily telling JJ that she's afraid of her (Emily's) secret being revealed. JJ tells her that the secret doesn't mean anything, and that they're still friends. Later, Emily calls JJ and tells her that she (Emily) told her (Emily's) mom about the secret, but it didn't go over very well.

This appears to be a role reversal created by JJ's subconscious, placing JJ's secret in Emily, and portraying Emily as the one with the secret. The phone text messages reveal that JJ is the one with the secret, and JJ is the one who came out to her mom, with it going poorly. But the phone calls act as if these things happened to Emily.