Oh, 12:07, you break our hearts.
We don't see the actual moment of Conor's mother's death, as if Ness wants to let Conor be alone with her. But we know what's coming, because he's set it up all through the book. Before Conor falls asleep in the monster's nest, he wants to ask why the monster always comes at 12:07, but he crashes before he can. The moment fits right in with the understated nature of the rest of the book. Part of its strength is that it never insults the reader's intelligence. Ness knows what he needs to tell us and what he doesn't.
As the clock creeps toward 12:07 on the last night of Conor's mother's life, Ness writes, "He knew it would come […] the moment she would slip from his grasp, no matter how tightly he held on" (32:48). Conor's nightmare becomes literal—he knows death will claim her, but he gets to keep holding her hand.
The last line of the book is, "And by doing so [holding her hand], he could finally let her go." It's the final paradox—the monster will pull her under, but Conor will still be hanging on. He'll stay on earth even as his mother leaves, still clutching her hand even as she slips from his grasp.