He opts to stay by her side. She dies.
And while he's there by her side, the thing he was working on seems to work on the lab animal. But of course, he's not there to see it, so there's no hurried rush to inject her with the serum, no rapid recovery, no happy ending. Instead there's crushing, irrational guilt. It doesn't matter that, as his mentor puts it, cures are not developed overnight; it only matters that it might have been.
Okay, you say, but what about the trippy bodhisattva in the bubble rushing through space? What about the conquistador searching for the Tree of Life in the Novis Mundi? Fictions. At a certain point in the story, Rachel Weisz gives Hugh Jackman a handwritten manuscript title "The Fountain." The story of the conquistador, as it parallels the life of her husband, is written in the manuscript. Before she dies, she tells Jackman to finish it.
He doesn't want to. He doesn't think he can. He's wracked with guilt. He's killed her through his lack of devotion, his decision to be with her instead of work for her. He's not worthy.
And then he finishes reading what she's written, and he sees that she had made peace with death. He sees that she believed that in death there is the seed of life. He sees that she wants him to live. And so he finishes the story. He takes it into the realm of metaphysical science fiction, where he, the traveller, floats through space along with the Tree of Life, seeking to penetrate into the heart of Xibalba, the Mayan Realm of the Dead, where the death of that star will reinvigorate the Tree, bringing them all back to life. He has the conquistador partake of the Tree of Life only to die and erupt in plant life, the world reborn. He envisions the death of the tree and the explosion of the star and the understanding that in the consumption of the phoenix in the flame lies its own rebirth.
He comes to grips with her death, and he demonstrates this, at the end of the movie, by planting a seed in her grave.
So there you have it. One story, three parts, two fictional, one factual. It's not that hard to follow, really. I think people are getting tripped up on the "centuries-spanning" thing because it's the easiest, laziest way to view the material, but really, that's just plain wrong.
*'My father used to say: "The first time someone calls you a horse you punch him on the nose, the second time someone calls you a horse you call him a jerk but the third time someone calls you a horse, well then perhaps it's time to go shopping for a saddle."'
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