This film unfolds through three interconnected narratives that traverse the era of the Spanish conquistadors, a futuristic setting, and a profound voyage through space aboard an ecospheric starship.
In the first narrative, the dedicated research oncologist, Tommy Creo, is determined to find a solution for brain tumors, which motivates him greatly due to his beloved wife, Izzi, who is suffering from cancer. While conducting experiments on rhesus monkeys, he faces setbacks, particularly with a monkey named Donovan. Driven by desperation, Tommy makes the risky decision to utilize a novel compound derived from a rare Guatemalan tree. The initial results are disappointing; however, Donovan undergoes an astonishing transformation—recovering from his injuries and significantly enhancing his mental faculties.
At home, Izzi reveals a mesmerizing golden nebula to Tommy, which she describes as Xibalba, the Mayan underworld. She also shares a book she is crafting about the conquistadors titled The Fountain. As evening falls, Tommy finds himself captivated by her narrative and eventually drifts to sleep while reading her work. The following day, upon waking, he discovers that Izzi has ventured to a museum to discuss the Mayan creation myth. Tragically, she suddenly collapses due to a seizure and is hurried to the hospital, where she shares a poignant moment with Tommy, declaring that she no longer fears death. Unwilling to accept her fate, Tommy immerses himself deeper into his research, pushing harder to uncover a cure.
As events unfold, Izzi experiences cardiac arrest, prompting Tommy to leave her side momentarily. When he regains his composure, he's informed by his colleague, Dr. Lillian Guzetti (Ellen Burstyn), that Donovan's tumor is diminishing. Elated, Tommy rushes back only to learn his wife's condition has worsened beyond help. During her funeral, Tommy passionately proclaims to Guzetti, > "Death is a disease, it's like any other. And there is a cure. A cure. And I will find it."
In the second narrative, set in 16th century Spain, the Grand Inquisitor, Silecio (Stephen McHattie), vilifies Queen Isabella, Izzi, branding her a heretic. As he gradually seizes control and eliminates her supporters, Tomas (also played by [Hugh Jackman]), a loyal conquistador, pledges to assassinate Silecio but is diverted by an urgent communique from Isabella. Tasked with an important mission, he embarks on a quest to locate the Tree of Life, with the help of Father Avila (Mark Margolis) and his fellow conquistadors, using a map hidden in a Mayan dagger. Throughout the treacherous journey to the New World, Tomas grapples with insubordination from his men, ultimately restoring order through lethal force as they finally reach their destination. Faced with the tree atop a tremendous pyramid, he confronts fierce Mayan warriors who claim the lives of his companions. As Tomas ascends the steps of the pyramid, he falls victim to a priest's blade.
In the third narrative, the astronaut Tom ([Hugh Jackman]) heads toward the golden nebula, accompanied by a living tree onboard his ecospheric vessel. Practicing meditation and tai chi, he keeps himself youthful with sap derived from the tree, yet he's haunted by visions of Izzi. As he navigates this profound journey, he desperately reassures the dying tree that it will eventually blossom again, despite his actions depleting its essence. The tree perishes, leaving Tom reflecting on the centuries spent in the void, longing to reunite with Izzi. In a moment of clarity, Izzi's spirit urges him to complete her book, The Fountain, leading him to confront his fear of mortality, allowing him the peace to finalize her story.
In a gripping resolution, instead of slaying Tomas, a Mayan priest recognizes him as "First Father," destined to sacrifice himself to create the world. After a brief hesitation, Tomas accepts his fate and administers the priest's sacrifice. Crossing through a threshold, he finally discovers the Tree of Life flourishing atop the pyramid. As he pierces it with the Mayan dagger, rewards of rejuvenation manifest as sap spills and brings forth new life—healing him with its magical properties. Yet, in a tragic turn, he collapses in anguish, his existence intertwined with leaves and flowers that consume him. In the future, the astronaut Tom, adorned with a ring from Isabella, enters the nebula, ultimately achieving harmony with his impending demise as Xibalba forms above him. The essence of Tom disperses, intertwining with the lifeless tree, rekindling it through his love and sacrifice. Finally, in modern times, Tommy is depicted planting a tree seed over Izzi's grave, striving to embrace the reality of her loss while honoring her memory.
