When this happens, everyone believes that Tom and the other boys have drowned.  Tom has snuck back to see what is going on.

When he gets back to his house, Aunt Polly and Mrs. Harper are all crying.  They're feeling so bad because of how their kids are dead.  They wish they'd treated the kids better.  As you might hope, Tom starts to feel a bit bad about this.  The book says that his heart gets to be full of pity for his aunt.

Of course, that doesn't make him stay and admit what had happened.  Instead, he kisses her as she sleeps and goes back to the island.