Conor wakes up from a nightmare about a monster at 12:07, the same time as always.
He finds a monster outside his window, but it's the wrong monster (not the one from the dream). This monster is actually a yew tree come to life, and it tells Conor it will tell him three stories over multiple nights.
He takes care of his mother, who's dying of cancer, until she gets so sick that his grandma has to come and visit.
Conor shuffles between his grandma's house and his mom's hospital room, with a brief visit from his dad, while his mother gets sicker and sicker. And sicker.
When the monster comes to visit, Conor listens to the stories, even though he thinks they're lame because they always have convoluted morals that are never what you'd expect.
He gets bullied at school and/or handled with kid gloves because of his mom's illness.
The monster helps him express his anger on two occasions: when he wrecks his grandma's living room and when he beats up his major bully, Harry.
Through all of this, he continues to have his nightmare. He knows the monster wants him to tell the truth about it, but he doesn't think he can.
After the monster has told the three stories, it demands that Conor tell the story of his nightmare, but Conor doesn't want to.
No choice, pal: the monster turns Conor's backyard into his nightmare, in which Conor tries to save his mother but can't.
When he admits to the monster that he failed to save her in part because he's exhausted and just wants her pain to end, the monster commends him for telling the truth and allows him to fall asleep in its branches.
At the end of the book, he goes to his mom's hospital room to be with her as she dies, and he tells her he doesn't want her to leave. Then he sits with her until she dies at 12:07.