This movie takes place in three interweaving narratives that encompass the age of the Spanish conquistadors, the near-future period and a journey through deep space in an ecospheric starship.
The scientist: Research oncologist Tommy Creo (Hugh Jackman) attempts to reverse brain tumors in rhesus monkeys through animal testing. His work is motivated by his cancer-stricken wife Izzi (Rachel Weisz). When the tests fail on a monkey named Donovan, Tommy is inspired to break medical protocol and use an untested compound derived from a Guatemalan tree. At first, the drug fails to stop the tumor's growth, but surprisingly rejuvenates Donovan, healing his wounds and improving his cognitive abilities.
At home, Izzi points out a golden nebula to Tommy, describing it as Xibalba, the Mayan underworld. She also shows Tommy a book she is writing, set in the age of conquistadors, titled The Fountain. When she goes to sleep, Tommy reads the book and falls asleep as well. When he wakes up, he finds that Izzi has gone to the museum. He meets her there, and she explains the creation myth of the Mayans. She suddenly collapses from a seizure and is rushed to the hospital. She tells Tommy, at her bedside, that she no longer fears death. Tommy does not accept this and returns to his lab, working harder to find a cure for Izzi's brain tumor.
During a visit, Izzi goes into cardiac arrest, and Tommy is forced to leave the room. Tommy's associate Dr. Lillian Guzetti (Ellen Burstyn) finds him in the hall and tells him that Donovan's tumor is shrinking. Tommy rushes back into Izzi's room with the news, only to find that his wife cannot be resuscitated. At Izzi's funeral, Tommy tells Guzetti, "Death is a disease, it's like any other. And there is a cure. A cure. And I will find it."
The Conquistador: In 16th century Spain, Grand Inquisitor Silecio (Stephen McHattie) demonizes the Spanish Queen Isabella (Rachel Weisz) as a heretic. He slowly acquires territories as part of his plan to take Spain from her, killing her followers along the way. Tomas (Hugh Jackman), a conquistador in the service of Isabella, plots to assassinate Silecio, only to be stopped by a subordinate, Captain Ariel (Cliff Curtis), bearing an urgent message from the Queen. Returning to Isabella's court, Tomas is given the mission of finding the Tree of Life. The tree's location is revealed on a hidden map displayed by a Mayan dagger stolen by Father Avila (Mark Margolis), whose Franciscan order backs the Queen.
Tomas journeys to the New World (America) with Avila and fellow conquistadores to find the tree. As the search drags on and the hardships of the quest multiply, the men mutiny; Tomas restores order by killing the ringleaders as Avila reveals that they have arrived at their destination. As Tomas approaches the pyramid atop which the tree grows, Mayan warriors attack the conquistadores. Tomas's last two men are killed fleeing the battle. Tomas is spared by the warriors, who force him to climb the pyramid. When Tomas reaches the temple at the top, he is stabbed in the abdomen by a Mayan priest.
The Astronaut: The astronaut, Tom (Hugh Jackman), travels toward a golden nebula in an ecospheric spacecraft, which also houses a living tree. Tom meditates in padmasana and practices tai chi. Kept young by compounds he produces from the tree's sap, Tom is haunted by visions of Izzi. He focuses on reaching the nebula, repeatedly assuring the tree that it will be reborn on arrival despite the amount of sap he has taken from it. Despite his assurance, the tree dies, leaving Tom to ponder the hundreds of years of travel that have been all to see Izzi again. Izzi haunts Tom in a vision and encourages him to finish writing her book, The Fountain. Tom faces his fear of death and accepts dying, allowing him to finally write the book's ending.
Instead of killing Tomas, a Mayan priest identifies Tomas as First Father, the deity who sacrificed himself to create the world. The Mayan priest in turn presents himself as a sacrifice, and Tomas hesitatingly slits his throat. Passing through a doorway, the conquistador finds the Tree of Life in a garden atop the pyramid. As he pierces it with the stolen Mayan dagger, its sap spills onto the ground, and a small plant instantly grows and blossoms where it fell. Taking this as a sign of rejuvenation, Tomas applies some sap to his abdominal wound, healing himself. He then greedily drinks the sap, stopping only when he begins to see Xibalba appear above him. His victory is cut short however, as he collapses in pain, leaves and flowers bursting from his body, burying him. The future Tom is then shown passing into the heart of the nebula, wearing a ring given to Tomas by the Queen of Spain, and entering Xibalba at peace with the thought of his imminent death. As Xibalba collapses and supernovas Tom's body is scattered into the dead tree rejuvenating it. In the present day Tommy is seen planting a tree seed over Izzi's grave doing his best to accept his wife's death.