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เรื่องราวของครอบครัวหนึ่งที่เกิดขึ้นในเมืองเล็กๆ ในเซ็นทรัลเท็กซัส ปี 1950 ที่มีลูกชายด้วยกันทั้งหมด 3 คน ได้แก่ แจ็ก (ฮันเตอร์ แม็กแครกเกน) อาร์แอล (ลารามี เอ็ปเพลอร์) และ สตีฟ (ไท เชอริแดน) โดยที่มีหัวหน้าครอบครัว คือ โอเบรียน (แบรด พิตต์)

เรื่องราวเป็นการติดตามความเป็นไปของ แจ็ก (รับบทตอนโตโดย ฌอน เพนน์) หนึ่งในพี่น้องสามคนของครอบครัวนี้ และความสัมพันธ์ของเขากับคุณพ่อที่เขาพยายามจะทำความเข้าใจและหาทางปรองดองคืนดี

Details of the plot released by sources involved in the production have been minimal. It is described as a 1950s period piece. The first official description of the film emerged from foreign sales agent Summit Entertainment's official website on September 21 2008 in the form of a thematic summary of the film describing it as the tale of a Midwestern boy's journey from the innocence of childhood to his disillusioned adult years as a lost soul in the modern world and his quest to regain meaning in life.

We trace the evolution of an eleven-year-old boy in the Midwest Jack one of three brothers. At first all seems marvelous to the child. He sees as his mother does with the eyes of his soul. She represents the way of love and mercy where the father tries to teach his son the world's way of putting oneself first. Each parent contends for his allegiance and Jack must reconcile their claims. The picture darkens as he has his first glimpses of sickness suffering and death. The world once a thing of glory becomes a labyrinth.

From this story is that of adult Jack a lost soul in a modern world seeking to discover amid the changing scenes of time that which does not change the eternal scheme of which we are a part. When he sees all that has gone into our world's preparation each thing appears a miracle?precious incomparable. Jack with his new understanding is able to forgive his father and take his first steps on the path of life.

The story ends in hope acknowledging the beauty and joy in all things in the everyday and above all in the family?our first school?the only place that most of us learn the truth about the world and ourselves or discover life's single most important lesson of unselfish love.

In an October 2008 interview production designer Jack Fisk a longtime Malick collaborator suggested that the director is attempting something radical. He also implied that details of the film are a close secret. In early March 2009 visual effects artist Mike Fink revealed to Empire Magazine that he was working on scenes of prehistoric Earth for the film.

The similarity of the scenes Fink describes to descriptions of a hugely ambitious project entitled Q that Malick worked on soon after Days of Heaven has led to speculation that The Tree of Life is a resurrection of that abandoned project. The website aintitcool.com has since reported that the prehistoric scenes are being filmed for a separate IMAX-specific project depicting the birth and death of the universe. That film is being described as not narratively connected to The Tree of Lifet rather they are thematically complementary pieces.