Darren Aronofsky wrote the screenplay and directed this film. It's beautifully filmed, but a mishmash of a story. I believe the confusion arises because of a detail that is a spoiler, so I'll put that at the end.
The trailer and advertising of the film market "The Fountain" as science fiction, and that's dead wrong. It's an aching romance story hanging on a quest.
Hugh Jackman plays Tomas, a doctor trying desperately to find a cure for cancer. His wife Isabel, played by Rachel Weisz, is suffering from the disease and has only a short time to live. She asks for more time with him and gives him a book she's written; he opens the handbound volume and begins to read as she sleeps.
We are taken from the present to Ferdinand and Isabella and the quest for the discovery of the Tree of Life in the New World, inhabited by the precolombian, prechristian "natives," and Tomas is now a conquistador, relentless and heartless in his search. Later we find ourselves in the far future, where Tomas still searches for the Tree of Life. Then we return to the present as Tomas plants a seed at his wife's grave.
Much happens despite my short description. This may be a film of the magical realism genre (or maybe not - who can tell?) where Aronofsky created a reality in which desire and longing can change reality. The problem is that the film remains indecipherable at normal viewing levels, and we're left with an experience more like 2001: A Space Odyssey - we leave breathless over the experience but clueless over what it meant. It's a great looking movie, but it may not make a lot of sense. I'd compare it to Donnie Darko - Aranofsky left too much out. But here's where my suspicion comes into play.
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In the opening scenes, we see Isabel ask for time with Tomas, and he's too busy. He gives her short shrift and sends her away so that he can continue his research. His research fails, of course, and Isabel dies. But that scene is shown three times, and in the repetitions, the rejection is softened, then eliminated. At the end, Tomas plants a seed at her grave that grows into a tree. The seed he plants, however, is not a seed but a dead husk. It's planted in the dead of winter. It cannot grow into a tree. My suspicion is that the film is Tomas's restructuring of his memory of his life. His search for a cure failed, he failed his wife by devoting nothing to her when she was dying, and Tomas is creating a fantasy where he spent his time where it would have done good - in loving care of his wife.
The conquistador's search and the futurist's search for the saving tree of life are metaphors of course for the physician's search for a cure. The problem is that all three searches are doomed to failure. The search is for the searcher, and Isabel is left to fend for herself. My final question is whether this ever sank in for Tomas, whether he realized his quest was better left undone, that Isabel should have mattered more. I think this is an issue broader than the movie, and if Aranofsky had been able to get this more front and center he would have had a great movie. When the quest becomes more important than the person, tragedy ensues.
This all ignores a side question - if the search is for a Tree of LIfe, why is the movie called "The Fountain"?