The Overstory introduces each of its nine main characters with their own section. The first part begins in the mid-1800s, following the Hoel family as Jørgen Hoel brings six chestnuts from New York and plants them at his new home in Iowa. One seedling survives and grows massive, even as a blight wipes out most of the country’s other chestnuts. Jørgen’s son buys a camera and begins taking a photo of the chestnut tree once a month. This ritual lasts for generations, up to the latest Hoel, an art student named Nicholas. Visiting the family farm for Christmas one year, Nick is stranded on the road by a snowstorm. When he returns the next morning, he finds his family dead, killed by a gas leak.
The narrative then shifts to China, where Ma Sih Hsuin is preparing to move to America to attend engineering school. Before he leaves, his father gives him their family’s treasures: three jade rings carved like trees, and an ancient scroll portraying Buddhist adepts. Sih Hsuin moves to America, changes his name to Winston Ma, and gets married. He and his wife Charlotte plant a mulberry tree at their home in Illinois. They have three daughters: Mimi, Carmen, and Amelia. Mimi attends college and studies engineering. She grows worried when Winston calls her one day and seems depressed, and a few months later he dies by suicide beneath the mulberry tree. Charlotte slips into dementia, and the Ma daughters divide up the family treasures.
Adam Appich grows up in the 1960s with four siblings. His father plants a tree when each child is born, and Adam’s is a maple. Adam doesn’t get along well with other children besides his sister Jean, but he becomes fascinated with studying insects. When he is thirteen, Adam’s other older sister Leigh goes missing. In high school Adam starts a business doing homework for his peers, but he lets his own grades slip. One day he starts reading a book on social psychology and becomes enthralled. When it is time to apply to college, he writes a personal letter to the book’s author, who teaches at Fortuna College.
Ray Brinkman and Dorothy Cazaly, an intellectual property lawyer and a stenographer, start dating and performing in amateur theater together. Ray is innocent and responsible, while Dorothy is more unpredictable. After they sleep together for the first time, Ray asks Dorothy to marry him. They break up and get back together several times, finally getting married on a whim while vacationing in Rome. They make a plan to plant something new in their yard every year on their anniversary.
As a young man, Douglas Pavlicek takes part in the Stanford Prison Experiment, a psychological study that soon turns to torture and abuse. Afterwards he enlists in the U.S. Air Force and becomes a sergeant in Thailand. One day his plane is hit by a missile. Douglas falls out of the plane and lands in an enormous banyan tree, injuring his leg in the process. He is rescued and discharged, and he returns to America. After a stint as a caretaker for an isolated horse ranch in Idaho, Douglas drives to Oregon. Beyond the edge of the highway he sees hillsides that have been entirely clear-cut, and he is disturbed by the sight. He then takes a job planting thousands of Douglas-fir seedlings.
Neelay Mehta is seven years old, the child of Indian immigrants, when his father Babul brings home an early computer kit that he is working on. Together Babul and Neelay assemble the computer, and Neelay becomes obsessed with programming it. One day in school a teacher takes his notebook with all his computing work in it, and he curses at her. Crushed by shame, Neelay climbs a tree and then falls, breaking his back and becoming paralyzed from the waist down. Neelay goes through high school in a wheelchair and is accepted to Stanford two years early, already a genius at coding. He soon starts designing computer games and giving them away for free. While researching for his latest game, he wheels his chair into Stanford’s outdoor terrarium and is stunned by the variety of alien-looking trees there. He receives a vision of what he must do: create a game that is an entire immersive world for its players.
Patricia Westerford grows up as a deaf child obsessed with plants. She is extremely close with her father Bill, who takes her along on his work trips visiting farms in Ohio. He teaches her all about trees. When Patricia is fourteen, Bill dies in a car crash. Patricia studies botany in college, and then goes to forestry school. While working on her research there, she discovers that trees can communicate with each other through the gases they release. She publishes an article about this that at first becomes popular, but then is brutally condemned by a few prominent scientists. Patricia loses her job and becomes depressed, almost committing suicide by eating poisoned mushrooms.
She then spends years working odd jobs and heading west. She starts working for the Bureau of Land Management (BLM), and while living alone in the woods, other scientists begin to publish articles that confirm and build on her previous work. She meets two men in the forest who tell her that her work has been vindicated, and she starts living and working at their research station. The station manager, Dennis, eventually asks her to marry him, suggesting that they could still live apart even as a couple. Patricia happily agrees.
The narrative then turns to Olivia Vandergriff, a college student studying Actuarial Science. She is failing her classes and spends most of her time partying, having recently gotten married to a fellow student on a whim. On the day of her divorce she gets high and takes a shower; she is then is electrocuted by a faulty socket in her house, and her heart stops. After seventy seconds Olivia’s heart starts again, and she senses mysterious beings of light trying to contact her. Soon they lead her to abandon her classes and drive west to join activists trying to save the redwoods in California. On the way, she stops at the Hoel farm where the old chestnut is dying and Nick is trying to get rid of his art. Olivia asks Nick to come with her, and he agrees, amazed and smitten. They soon find their way to a group called the “Life Defense Force” that is committed to saving the redwoods.
At the same time Mimi and Douglas are brought together when a pine grove outside Mimi’s office is cut down in the middle of the night, enraging both of them. Together they start joining various activist events defending trees, and both are arrested and physically abused by police. They too make their way to the Life Defense Force.
Meanwhile Neelay starts his own company and becomes fantastically wealthy and successful with his immersive Mastery games, constantly building richer and more complex worlds with his coding. Patricia writes a best-selling book called The Secret Forest, all about how trees communicate. Adam decides to write his dissertation on the psychological profiles of environmental activists, and he begins interviewing people. Dorothy and Ray try to have a child but cannot, and in their dissatisfaction, they dive into reading and other hobbies. Soon Dorothy starts having an affair.
Nick and Olivia volunteer to take a turn squatting among the branches of a redwood called Mimas to prevent it being logged. They are supposed to only be there for a few days, but their vigil extends for months, and they adjust to an entirely new sense of time living alone in the tree. Patricia is invited to be an expert witness at a trial about logging rights, and she manages to temporarily stop the cutting of new lands. Ray and Dorothy have a fight and she asks to get divorced, but then Ray suddenly has a brain aneurysm and almost dies. Mimi is fired from her job after her latest arrest.
When Nick and Olivia have been in the tree for almost a year, Adam joins to interview them. While he is there a helicopter threatens them and they finally come down, admitting defeat. Mimas is cut down as the three are sent to jail. Afterwards Adam joins the Life Defense Force as well, and the group joins a new community protesting logging in Oregon. When their latest occupation is easily defeated and their members injured, Mimi, Douglas, Olivia, Nick, and Adam decide to take matters into their own hands and begin a new campaign of burning down logging equipment. The group decides to finish one last arson job in Idaho, but an explosion goes off sooner than planned, mortally injuring Olivia. The others try to tend to her, but when she dies they place her body in the flames and flee.
In the aftermath of Olivia’s death, the members of the group part ways, some of them changing their names and others going into hiding. Adam returns to graduate school and later becomes a respected professor in his field. Nick lives a transient life, longing for a message from Olivia and continuing to make activist art. Mimi changes her name and becomes a therapist in San Francisco, specializing in a therapy that involves connecting with the patient through sustained eye contact. Douglas lives as a caretaker for a ghost town in Montana.
Meanwhile Dorothy takes care of Ray after his aneurysm, as he is no longer able to speak clearly and cannot move. Together they become intrigued by the plant life in their backyard and learn to identify trees. Patricia starts a vault to preserve the seeds of trees that will soon be extinct, and she travels around the world both raising money for her project and collecting new specimens. Neelay becomes dissatisfied with his Mastery games and wants to start something different, a game about learning to preserve the natural world as it really is on Earth.
A tourist at Douglas’s job finds his journal and reports him for arson. To save Mimi from arrest, Douglas decides to identify Adam as an accomplice. Neelay breaks with his company and begins work on a new game, first creating artificial intelligences to learn everything they can about Earth’s biome. Patricia is invited to give a talk in front of a crowd of luminaries. In her speech, she discusses what people can truly do to save the world. While she plans to kill herself in front of the crowd (demonstrating her answer to how humanity can save the world), she is stopped by Neelay, who is in the audience. Adam pleads guilty to his crimes and is sentence to 140 years in prison. Ray and Dorothy decide to let their suburban yard grow wild, slowing their lives to watch all their trees grow and resisting outside pressures to mow everything down. Mimi realizes what both Adam and Douglas did for her and achieves a kind of enlightenment beneath a pine tree in a city park, now able to hear the voices of the trees around her. Nick, meanwhile, continues to make art, finishing with an enormous sculpture spelling out the word “STILL” that is meant to be seen from space.