Ernst Toller, portrayed by an unnamed actor, is the pastor of the historic First Reformed Church in Snowbridge, New York, grappling with a profound crisis of faith. The narrative begins with Toller documenting his thoughts in a journal, a project he intends to destroy after a year of reflection. This church, originally a pivotal stop on the Underground Railroad, now finds itself struggling with dwindling attendance under Toller's guidance, having veered away from its roots in Calvinist theology to become primarily a tourist destination.
Haunted by the loss of his son, Joseph, who was a casualty of the Iraq War, Toller also battles his own alcoholism. His journey toward deeper spiritual comprehension leads him to explore the writings of Roman Catholic authors like G. K. Chesterton and Thomas Merton, alongside mystical texts such as The Cloud of Unknowing. In search of solace, he reaches out to Abundant Life, a prominent evangelical megachurch in Albany that oversees First Reformed.
His life takes a pivotal turn when he is approached by Mary Mensana, who seeks guidance for her husband, Michael, a fervent environmentalist. Michael's radical views put Toller in a moral quandary as he reveals his desire for Mary to have an abortion, expressing his belief that bringing a child into a world devastated by climate change is cruel. When Mary finds a suicide vest belonging to Michael, Toller takes it, vowing to counsel him. Despite contemplating alerting the authorities, Toller hesitates, fearing it might exacerbate Michael's fragile mental state.
Tragically, before their next session, Toller discovers Michael has taken his own life with a shotgun. In line with Michael's last wishes, a memorial service is held at a local toxic-waste site, where his ashes are scattered. Meanwhile, preparations for First Reformed's 250th anniversary service—a significant event featuring local dignitaries and Edward Balq, a financial supporter of the church with a stake in climate pollution—are underway. Toller and Balq clash over their differing stances on climate change, Toller advocating for Christian stewardship while Balq dismisses it as overly complex.
In the midst of personal turmoil, Toller seeks medical attention due to recurring physical pain, and tests hint at possible stomach cancer. He discovers Michael's laptop, which he took to protect Mary from the consequences of Michael's radical beliefs, and dives into research concerning Michael’s fears about Balq’s factory. One evening, Mary visits Toller in the church's parsonage, where they share a moment of intimate connection reminiscent of Michael and Mary’s past.
As the anniversary service approaches, Toller implores Mary not to attend. In a drastic turn of events, he dons the explosive vest meant for Michael during the ceremony but ultimately substitutes it for barbed wire in a symbolic act of self-sacrifice. Just as he prepares to consume a glass of drain cleaner, a pivotal moment occurs—Mary interrupts him, and their passionate embrace leads to an abrupt and haunting conclusion as the screen fades to black.
