Oskar Schell is a super-smart nine-year old grieving the loss of his father, Thomas, who was killed in the World Trade Center attacks on September 11, 2001. He's feeling depressed and anxious, and feels angry and distant towards his mother. He's been pretty traumatized by his Dad's death and is afraid of just about everything.
And he has a terrible secret. When he got home from school on September 11, he listened to voice messages his Dad left on the answering machine from the burning World Trade Center. His Dad then called one last time, but Oskar was too afraid to pick up, and the line went dead. He's been so guilty about that since it happened that he hid the answering machine and hasn't told anyone about the messages.
One day, Oskar finds a key inside a vase in his father's closet. Was the key a message from his father? The key's in a little envelope with the word Black on it. Oskar realizes this must be a name, and he decides to track down every person in New York City with the last name Black. (The Yellow Pages wishes he would just let his fingers do the walking but Oskar's scared of phones.)
None of the Blacks know anything about the key, but a Mr. Black (we never find out his first name), who's never left his apartment in 24 years, agrees to help Oskar on his search. He visits all the Blacks in all the boroughs. It takes him eight months.
Oskar goes to his Grandma's apartment and talks to her mysterious renter, who, unbeknownst to Oskar, is Oskar's Grandpa. Oskar's grandfather had abandoned his grandmother when she became pregnant with Oskar's Dad. He couldn't bear loving anyone again (he had lost everyone he loved in WWII) but wrote letters to his son throughout his life, never mailing them. He returned to the U.S. just before September 11 to reunite with his family, but too late to meet his son, Oskar's dad. Grandpa moves back in with Grandma and they resume a pretty weird relationship.
Oskar tells the renter the whole story about his Dad and the search. In the meantime, Oskar checks the phone and gets a message from Abby Black, the second Black he spoke with. It just so happens that her husband, William, knows what the key belongs to: his own dead dad's safe deposit box. Oskar's kind of disappointed that the key didn't have much to do with his own dad at all, and he returns the key to William.
Oskar finds out that all the Blacks he visited have known who he was the whole time, because his Mom found out about Oskar's quest and called them all ahead of time.
With his search ended in disappointment, Oskar decides to dig up his Dad's empty coffin and asks the renter for help. Together, they go to the cemetery. The renter brings two suitcases filled with all the unsent letters he wrote to his son and buries them in the coffin. This seems to be a turning point for Oskar, who's able to move forward a little from his grief and loss and reconnect with his mother.
Finally, in a long letter from Grandma to Oskar, we find out about how Grandpa and Grandma grew up in Dresden, Germany, and both survived the firebombing of the city, although neither of their families did. Grandma knew that Grandpa was in love with her sister, Anna, but she married him anyway. She accepts it when he comes back to her on September 11 because she doesn't want to be alone. When he tries to leave her again, they both go to live at the airport together. Yes, at the airport.
In the end, Oskar is back to square one. He hasn't come to any profound conclusions about his Dad. He has a series of photos of a man falling to his death from the World Trade Center. He puts them in reverse order, so when he flips them (making this The Saddest Flipbook Ever©) the man falls up back into the building, and Oskar can imagine his Dad is safe.