I have a theory about this film that should necessitate some research except that I'm too lazy. I suspect that writer/director Darren ("Pi") Aronofsky discovered Buddhism or Hinduism or met the Dalai Lama or sat through a Steven Seagal film marathon or made a pilgrimage to Tibet in around the same time that he met and fell in love with his wife, Rachel Weisz. Thus, he decided to inflict his "revelations" about religion and love on the public.
Essentially, this entire film is Aronofsky's obsession, through Hugh Jackman, of his love for his wife and his ruminations on various spiritual principles and the combination of both. Since there are three stories here that take place in three distinct periods in time, roughly 16th century, 21st century, and 26th century, it's not hard to surmise that the central character Tomas/Tommy/Tom Creo (Hugh Jackman) is either the same man or a reincarnation. Since there's no direct explanation of how Tomas gets from one time period to another, reincarnation is a better explanation, thereby posing the idea that one's experiences could be essentially replayed throughout time or that one can be reborn. These are principles of one of those foofy religions, though I don't know which one exactly.
Frankly, I think getting off in public over the fact you married a hot, famous woman is kind of rude. Why couldn't Aronofsky and Weisz celebrate their love by doing what everyone else does and film themselves having sex?
Just to summarize, in the 16th century, Tomas (Hugh Jackman) is a conquistador and Queen Isabel (Rachel Weisz) assigns him to go find the tree of life and bring back its secrets. In the 21st century, Tom Creo (Hugh Jackman) is a doctor trying to find a cure for his wife's brain tumor. His wife's name is Izzi and she's played by Rachel Weisz. In the 26th century, Tommy (Hugh Jackman), is sailing through space in a glass ball with a tree in hopes of reaching a nebula. The tree is played by Rachel Weisz.
Just guessing, but the first time period represents hope, the second reality/loss, and the third memory and/or acceptance. Or something like that. In the first, Tomas has the potential to find the secret to living forever and have the Queen. In the second, instead of spending time with his wife, he obsesses over a cure. In the third, he's literally trapped by memory.
Aronofsky does lots of visual stuff with the camera to cover up the fact that his spiritual journey may have consisted solely of reading some cheap ass self-help book on grieving. After seeing this, I actually went out and bought a cheap ass self-help book on pain management. It didn't help.
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