When her mother dies, twelve-year-old Willa feels lost and alone except when she connects with things her mom loved about the wonders of the ocean as a marine biologist.

While on a whale-watching excursion with her dad, who is trying to cheer her up after Willa is sent to live with him and his new family, Willa is alone on one side of the boat when she sees a humpback whale. Her awe and wonderment about this massive and beautiful creature turns to shock when the whale communicates with her, introducing herself as Meg and exchanging small talk. Willa asks if they can talk again, and Meg tells her that if she goes to the edge of the shore and calls out to her, she'll reply. Whales, after all, are very social creatures and communicate by sounds that can travel for miles, underwater.

As their friendship develops, Willa views Meg as a trusted confidant who offers sound advice about dealing with a nemesis at school and trying to figure out why her best friend, Mark, is keeping secrets about his family life—all the kinds of talks her mom would normally have with her. She also learns about how similar whales are to humans in caring deeply for their babies, creating communities called "pods," and even singing.

When a blue whale washes up on shore and dies, the townspeople jump into action with opinions about what to do with it. Blue whales are the largest animals known to have ever existed, so there is no simple solution. Some are advocating blowing up the whale, some want to cut it up and drag it out to sea, others say let it rot on the obscure beach. Willa is outraged by what she views as inhumane treatment of the deceased whale and vows to do something about it, which is precisely what her mom would have wanted. She knows this is a problem she can't tackle alone, though, and enlists her friends, family, and the City Council to rescue the body of the whale and donate it to the local university where her mom taught for further study and to display the bones.

Feeling good about getting her community to band together in service of science and conservation, Willa returns to the shore to tell Meg about her amazing experience. Her joy is tempered with sadness when Meg tells Willa that it is time for her pod to migrate, but it's okay to say goodbye because they will always be connected in a special way in their hearts because they care about each other and showed it by listening and learning about each other.

Willa and the Whale is a poignant story about caring and loss and the deep connections that make us human.