Bixby Alexander Tam, a third-grader on the autism spectrum known to everyone as Bat, faces a summer full of goodbyes he is not ready to make.
On the first Monday in June, with only four days left in the school year, Bat sits with Babycakes, the class rabbit, at the back of his teacher Mr. Grayson's classroom. Mr. Grayson offers to let Bat take Babycakes home for the summer, hoping the rabbit's company will ease the difficulty of releasing Thor, the orphaned skunk kit Bat has been raising, into the wild. Bat declines, explaining that Thor needs him and he cannot be the best caretaker for two animals at once. The mention of saying goodbye to Thor causes him to make an involuntary high-pitched sound. He rocks back and forth, a self-soothing behavior he uses when distressed, feeling that time is moving much too fast.
When his best friend, Israel, arrives at school, Bat proposes that Israel take Babycakes for the summer. Israel reminds Bat that he is leaving the day after school ends to visit his cousin Robert in Canada. Bat admits he will miss Israel, noting small details he knows he will miss: Israel's curly hair, his toothy smile, his wrinkled T-shirt. Bat and his mom have a comforting daily routine: Each morning Bat feeds and grooms Thor, then brings him in a kitty carrier to the car. Mom drops Bat at school and takes Thor to her veterinary clinic, where the skunk sleeps in a crate lined with one of Bat's unwashed shirts.
At home, Bat and his older sister, Janie, bake chocolate cupcakes. That evening, eating them in the backyard near Thor's Garden, the vegetable patch Bat planted with Israel, Bat notices a pumpkin plant his mom added. It saddens him because by fall, Thor will have been released and will never see a jack-o'-lantern carved from it. Janie follows him to his room and offers her pink hairbrush as a gift for Thor. Bat brushes the skunk, who relaxes and enjoys it, and Janie snaps a picture with the digital camera she carries everywhere.
Bat resolves that his classmate Jenny should be Babycakes's summer caretaker, and Mr. Grayson offers the rabbit to Jenny. Bat panics when Jenny mentions her cat once flipped baby tortoises onto their backs, fearing her home is unsafe for Babycakes. Mr. Grayson declines but promises to give Jenny's family Bat's mom's phone number. On the last day of third grade, Bat spends the yearbook-signing period sitting with the rabbit. Mr. Grayson tells him this will be Babycakes's third summer going home with a student and that the rabbit returns safely each fall. Bat realizes he will also miss Mr. Grayson, who assures him he can visit anytime.
That weekend, Dad announces a dinner to meet a new friend. Janie develops a sudden headache and refuses to go, so Dad cancels. The next morning, the three bike to a doughnut shop where Suzette, Dad's friend, is waiting. Janie refuses to shake Suzette's hand, angry that Dad surprised them. Suzette gently scolds Dad for not warning the children. Later, at the city pool, Dad apologizes and promises no more surprises. Janie and Bat negotiate that their bike rides and doughnut outings remain just for the three of them, and Dad agrees.
With Janie taking swim classes, Bat begins spending summer days at Mom's clinic. He feels pride seeing the sign reading "Valerie Tam, DVM," standing for Doctor of Veterinary Medicine, and imagines one day working alongside her. He helps Laurence, the veterinary technician, with baths, nail trims, and dog walks.
One morning, Jenny bursts through the clinic door in tears, her grandmother behind her carrying Babycakes wrapped in a towel. Bat's mom diagnoses the snuffles, a respiratory infection in rabbits that has caused an ear infection and a head tilt. Bat initially blurts that he should not have let Jenny be caretaker, but after examining Babycakes's well-brushed coat and healthy weight, he tells Jenny she has taken good care of the rabbit. Babycakes recovers after four nights at the clinic on antibiotics. On a follow-up visit, Jenny asks how much longer Bat gets to keep Thor. Though Bat resists the topic, he finds relief when Jenny admits she would miss her own pets terribly.
Israel writes Bat a letter from Canada about Robert's juggling talents and a story about a tamed bird that returns to visit its former caretaker each year, suggesting Thor might do the same. Bat worries Israel might replace him as best friend. With Janie's help, he revises his reply into a proper letter, adding details and questions.
On a sweltering day, the heat and noise of errands overwhelm Bat. At home, he retreats to his room, where Thor senses his distress and comes to the gate of his enclosure. Bat picks him up, lies down, and begins to cry. Thor sniffs and licks Bat's tears until Bat gradually calms, and they fall asleep together. All summer, Janie captures moments like these with her camera. Yet an image haunts Bat all season: Thor's black-and-white tail disappearing into a bush, leaving him forever. When the image comes, he pulls his shirt collar into his mouth and rocks. Mom opens her arms, offering a hug without forcing contact, and the part of Bat that wants the hug wins.
Israel returns from Canada, and the boys visit Babycakes at Jenny's house. The rabbit is healthy and bright-eyed. Over cookies, Bat asks if Robert is Israel's best friend now. Israel firmly reassures him: Robert is his cousin, but Bat is his best friend. On the drive to Bat's house, Israel says he is worried about what will happen when Bat has to let Thor go. Tom, Israel's dad, clarifies that Israel is worried about Bat himself. Bat admits he will be really, really sad. Israel puts his arm around Bat's shoulders.
When they arrive, Dad's car is unexpectedly in the driveway. Inside, Mom, Dad, and Janie are seated at the kitchen table for a family meeting about Thor. Bat asks Israel to stay, and Mom agrees. Bat declares that he does not want to release Thor and that they belong together. Janie reveals she wrote to Dr. Jerry Dragoo at the Dragoo Institute for the Betterment of Skunks and Skunk Reputations, whom Bat had previously contacted about Thor. She included photographs from the summer and a description of Bat's gentle care. Dr. Dragoo responded that when a skunk and caretaker are as bonded as Bat and Thor, they should remain together. Dad shares that he consulted Dr. Ted Stankowich, a skunk expert Suzette helped him reach, who confirmed that a skunk as bonded as Thor would likely not survive well in the wild. Dad tells Bat he is proud of him. Mom agrees: Bat and Thor belong together.
Overwhelmed with emotion, Bat's hands begin to flap. He excuses himself to his room, calms down, and picks up Thor, who nuzzles into Bat's neck. Bat carries the skunk back to the kitchen on his shoulder and announces to his family and best friend that they are all there now, the whole family. The kitchen is full of sunlight, and Bat knows he is exactly where he belongs.