Embedded with exceptional visual effects and deep conceptual thought, this extraordinary family drama begins with a quotation from the Book of Job: "Where were you when I laid the foundations of the Earth?... When the morning stars sang together, and all the sons of God shouted for joy?"
A mysterious, wavering light, resembling a flame, flickers in the darkness. Mrs. O'Brien recalls a lesson taught to her that people must choose to follow either the path of grace or the path of nature. In the 1960s, she receives a telegram informing her of the death of her son, R.L., aged nineteen. Mr. O'Brien is notified by telephone while at an airport. The family is thrown into turmoil.
In the present day, the O'Briens' eldest son, Jack, is adrift in his modern life as an architect. One day he apologizes to his father on the phone for an argument about R.L.'s death. In his office, Jack begins reflecting and shots of tall buildings under the sky, Jack wandering in the desert, trees that stretch from the ground up to the sun high in their leaves and scenes from his childhood in the 1950s that all link together and lead back to the flame are seen.
From the darkness the universe is born, the Milky Way and then the solar system form while voice-overs ask existential questions. On the newly formed Earth, volcanoes erupt and microbes begin to form and replicate. Sea life is born, then plants on land, then dinosaurs. In a symbolic first act of compassion, a dinosaur chooses not to eat a weakened creature that is lying on the side of a river bed. An asteroid tumbles through space and strikes the Earth, causing the Cretaceous–Paleogene extinction event.
In a sprawling neighborhood in Waco, Texas live the O'Briens. The young couple is enthralled by their new baby Jack and, later, his two brothers. When Jack reaches adolescence, he is faced with the conflict of accepting the way of grace or nature, as embodied by each of his parents. Mrs. O'Brien is gentle, nurturing, and authoritative, presenting the world to her children as a place of wonder. Mr. O'Brien is strict and authoritarian, and easily loses his temper as he struggles to reconcile his love for his sons with wanting to prepare them for a world he sees as corrupt and exploitative. He laments his decision to become an engineer instead of pursuing his passion for music. He tries to get ahead by filing patents for various inventions.
Jack's perceptions of the world begin to change after one of his friends drowns at the pool and another of his friends is burned in a house fire. He becomes angry at his father for his bullying behavior and begins to keep a running tally of Mr. O'Brien's various hypocrisies and misdeeds, lashing out at his mother for tolerating such abusive behavior.
One summer, Mr. O'Brien takes a long business trip. While he is away, the boys enjoy unfettered access to their mother, and Jack experiences the first twinges of rebelliousness. Goaded by other boys his age, Jack commits acts of vandalism and animal abuse. He later trespasses into a neighbor's house and steals her sheer nightgown. Jack is confused and angered by his feelings of sexuality and guilty trespass. He throws the stolen lingerie into a river to rid himself of it.
Mr. O'Brien returns home from his unsuccessful business trip. Shortly thereafter, the plant that he works at closes and he is given the option of relocating to work in a thankless position within the firm or losing his job. He and his family pack up to move to the new job location. He laments the course his life has taken, questioning whether he has been a good enough person. He asks Jack for forgiveness for his harsh treatment of him.
In the present, adult Jack leaves work. Riding the elevator up, he experiences a vision of following a young girl across rocky terrain. Jack tentatively walks through a wooden door frame erected on the rocks and sees a view of the far distant future in which the sun expands into a red giant, engulfing the earth and then shrinking into a feeble white dwarf. Someone says "follow me" in the darkness, which is ended by the lighting of two candles.
After emerging from rustic doors, Jack follows the girl and then a young version of himself across surreal landscapes. On a sandbar, Jack sees images of death and the dead returning to life. He is reunited with his family and all the people who populate his memory. His father is happy to see him. He encounters his dead brother, whom he brings to his parents. Accompanied by a woman in white and her younger self, Mrs. O'Brien looks to the sky and whispers, "I give him to you. I give you my son."
Jack's vision ends and he leaves the building smiling.
The mysterious wavering light continues to flicker in the darkness.