Ok, I'm bored at work and have decided to write an explanation for one of my favorite movies, The Fountain. It's not a movie that is easy to understand and actually you will have to pay close attention and use your head to really understand what it is about.
The story is actually very simple. The movie is about Tom and Izzy who are married and trying to cope with Izzy's terminal brain cancer. Tom is a scientist who is studying cures for cancer in an effort to keep Izzy alive.
The movie opens up with Tom dreaming about a book Izzy wrote to cope with her impending death, the book is titled "The Fountain". In the book Thomas (the conquistador) symbolizes Tom in the present, Queen Issabella symbolizes Izzy, and the archbishop symbolizes Izzy's cancer as he is trying to kill Queen Issabella. Tom is dreaming about the end of the book in which he reaches the top of the Mayan temple where the Tree of Life is hidden. He wakes up just as the mayan shaman is about to kill Thomas.
Here is the confusing part. The entire movie actually takes place sometime around the year 2500. Everything else is either a flashback to the past (our present day) or Tom remembering Izzy's book. When Thomas awakens he is in a spaceship which is headed for a dying star wrapped inside a supernova. The star is called Xibalba, which in the movie is the Mayan underworld where people go to die. The spaceship is an ecosphere so it does not appear in the form of the spaceship people would expect, but I think the ecosphere is a brilliant concept.
Tom is haunted by images of Izzy that seem lifelike. The reason they are lifelike is that Tom eats from a seeded Tree of Life which was buried over Izzy's grave. Every time he injests the tree he injests part of Izzy. Didn't catch that Izzy is part of the tree in the spaceship? Watch the scene where Tom is washing her, as he moves the sponge over her body it morphs from her body into the tree of life. There are more things that hint to this in the movie that I will touch on later.
Tom has forgotten why he is traveling to Xibalba so Izzy forces him to remember his past from 500 years ago ("I trust you, take me back"). All of the present day you see from here on out is Tom remembering it from the future. Cut to present day where Tom is working on a cure for cancer. Izzy has accepted her impending death, while Tom has not. Instead of being gloomy about it, Izzy searches for spirituality and for ways to help Tom deal with it. Izzy makes sure that she is buried on a farm and tells Tom a story about how the mayan guide she had during her trip to Guatamala. The mayan guide buried a tree over his father's grave so that the tree would absorb him, birds would feed from the tree, and his father would "live forever".
Izzy finally goes into cardiac and Tom is unable to save her. One of the doctors tells him at this very moment that he discovered the cure for cancer. Tom rushes back to try and revive Izzy, however he is unable to do so. At the same moment he realizes he is unable to revive her, he is brought out of his recollection of the past because the tree of life is about to die. The tree of life (Izzy) dies in the future so once again Tom has failed to save Izzy. Imagine spending 500 years of your life trying to get your significant other to be reborn and she dies
AGAIN just before you can save her. His heartbreak is quite understandable once you realize all he has been through.
Izzy then comes to Tom while he is grieving and makes him understand what he is here to do. Tom understands that he will die as Xibalba explodes so he finally finishes the last chapter of Izzys book, in his head. Notice how the camera zooms into his forehead which clearly implies that everything you see from here until Tom's death is Tom completely Izzy's book mentally. Tom finishes the book by having the mayan shaman realize that Thomas is a reincarnation of their first father. The shaman lets Thomas kill him and reach the tree. After drinking the sap, Thomas dies and becomes part of the surroundings of the tree instead of living forever.
Finally Xibalba explodes and Tom dies with his ashes and essence falling back on the tree of life. The tree of life is reborn using the power from the exploding star and Tom joins Izzy in the afterlife. The movie ends with a scene that shows Tom burying a seed from the tree of life over Izzy's grave.
How do we know that Izzy is the tree of life in the spaceship?:
1) Izzy morphs into the tree during the bath scene
2) Tom says the exact same lines to the tree that he said to Izzy in the past and touches the tree in the same manner he would caress Izzy.
3) When Tom kisses Izzy's neck the hairs on her neck are very similar to the hairs that move when he touches the tree of life.
4) When the tree dies, Tom is extremely distraught, kisses the tree. Is this because Tom is a tree hugger? NO, it's because the tree holds Izzy's essence/soul and she has died again.
5) Finally we see the scene where Tom buries the scene and looks up to Xibalba. This is eventually where he will travel after 500 years.