Several secrets lurk within the pages of Scar Island, and their eventual revelations drive the plot and themes of the story. Jonathan guards the novel’s biggest secret: the sad story of why he was sent to Slabhenge Reformatory. The other boys talk about why they were sent to the school: Jason stole cars, Walter stole a purse to give his mom for Mother’s Day, Miguel skipped school. But when anyone asks Jonathan what he did, he finds a way to change the subject or remains silent. He makes sure no one sees the scars on his arms, and when he finds the key to the Admiral’s office, he keeps it to himself so that no one can go into the office and see his file. The revelation of Jonathan’s secret at the end of the story helps him redeem himself because it forces him to come to terms with what he has been hiding inside, and he sees that others react to the full truth with empathy instead of judgment. Thus, the disclosure of his secret is a key factor in Jonathan’s self-redemption.

The owners and operators of Slabhenge keep the Hatch a secret, telling the boys it is a monster and not a door to hold back the rising sea.