NOTE: Spoiler #56 sent in by Brentage5000."So he drove out the man; and he placed at the east of the garden of Eden Cherubims, and a flaming sword which turned every way, to keep the way of the tree of life."
After seeing this written across the screen in a nice flowing script, we see a conquistador named Tomas (Hugh Jackman) praying to God and carefully handling an ornate ring. He remembers being given the ring by the beautiful Queen Isabella of Portugal (Rachel Weisz), crosses himself, and carefully puts the ring back in its cloth wrapping. He goes to rejoin his two remaining compatriots in a long stone corridor in the middle of the South American jungle. One of them warns that they are about to walk into a trap, but Tomas says he already knows. They head forward and are set upon by dozens of Mayan warriors. Tomas urges his men to stand, but they chicken out and are taken out. Tomas fights briefly, but he is soon overwhelmed. His back is put to the wall by the warriors when they stop advancing. He turns and sees steps leading to the top of a pyramid. He ascends them and finds...another corridor, inside of which is waiting a heavily decorated Mayan priest. The priest says that First Father sacrificed himself and attacks Tomas. He stabs him and tells Tomas that death will him in awe and swings his axe. Tomas screams and--
We see, in the far future, a man named Tommy (Hugh Jackman) waking up screaming from a frightening nightmare/memory. He looks around and we see that he is in a floating bubble with a nearly dead tree inside it. The bubble is floating towards something and we see Tommy scrape a piece of bark off the tree (which has hairs on it for some reason) and eat it. We flash back for a second to see old and bald Tommy arguing with his wife Izzi (Rachel Weisz) over whether or not to go out walking in the new snow, but Tommy says he's too busy and Izzi leaves and heads off. Tommy sighs and (in the bubble) apologizes to the tree. Izzi appears behind him and he apologizes to her too, but he says they're almost there.
Suddenly we're once again seeing Izzi arguing over whether or not her husband, Dr. Tom Creo (Hugh Jackman), should go out walking in the fresh new snow with her, but he says he's too busy. She heads out, and he apologizes to the air and heads after her, but is stopped by one of his colleagues, who tells him that some guy named Donovan is ready to be operated on. Tom goes into the prep room and puts his ring above the sink before putting on his gloves. He goes into the room and starts operating when Donovan suddenly starts flatlining. They bring him back but Tom is still upset. He is talking with his partners when suddenly he has the idea to use some plant substance found on a tree in Guatemala. One of them, Gideon (Sean Patrick Thomas) realizes that this would merge with the subject's DNA, and soon they're tracking down everything they can regarding it. They mix it up and inject it into Donovan (who we now see is a monkey), and he recovers nicely. Unfortunately for Tom, his supervisor, Dr. Lilian Guzetti (Ellen Burstyn), gets wind of this and chews Tom out for being reckless, although he ignores her as being too cautious. To make a bad day worse, Tom also manages to lose his wedding ring from the operating room, although everyone reassures him they'll keep an eye out for it.
That night, we see Tom arrive home at his apartment. He calls out for Izzi and after a tense minute where he can't find her she calls to him from the fire escape. He pokes his head out and is immediately rewarded with a snowball upside the head. Izzi drags him outside and shows him a nebula she found that -- according to Mayan historians, which she's reviewing for a book she's writing -- is known as Xibalba. She tells him that it's a dying star in a nebula and that it's the same star Mayans viewed as the gateway to the underworld. Izzi asks Tom what he thinks of the odds of that but he is saved from answering by noticing that she's not wearing shoes. He gets her inside and after a brief shot of the bubble floating upwards towards a dying star we see Tom giving Izzi a bath. They play around a little bit and Tom moves to get something when Izzi suddenly calls him back and asks him to heat the sponge. He does so and scrubs her legs with the scalding hot sponge but she doesn't feel it. Izzi says that she's felt this way for a while and that she feels different inside now, and Tom reassures her. He leans down to kiss her, and she yanks him into the tub, where the two have some hot tub sex.
Some time later, Izzi and Tom are drying off when Izzi shows off her book to Tom. She tells him it's called "The Fountain" and says that she's nearly finished and she wants him to read it. Before he can answer the phone rings, and it's Gideon. He says that there's been a major development with Donovan and he needs to get to the hospital right away. Izzi begs him not to go, but of course he does. When he gets there he finds out that Donovan -- previously a very old monkey with a tumor -- is now a very youngish monkey. Despite his amazement, he asks for the status on the tumor and is told that there's no change. He shakes his head and goes to work trying to figure this out. He doesn't return home until much later and finds Izzi asleep. He kisses her and says that everything is alright. He heads for her book, picks it up, and goes into his study and starts reading...
We see Tomas praying at church when he is suddenly approached by a soldier, who gives him an update on something. Elsewhere, we see the head of the inquisition, a man named Silecio (Stephen McHattie), preaching to a bunch of recently converted people hanging from chains. Not far away, we see Tomas aiming a crossbow at Silecio's head when he is interrupted by Captain Ariel (Cliff Curtis), one of his subordinates. Ariel says that the queen has requested him immediately and after some reluctance, Tomas retreats and heads for the palace. Once there, Queen Isabella introduces him a priest named Father Avila (Mark Margolis) who has come into possession of a dagger that when placed against a map of New Spain (Mayan territory) shows the location of a hidden pyramid atop which lies the Tree of Life (not to be confused with the Tree of Knowledge, which Adam and Eve ate from). Isabella removes one of her rings and gives it to Tomas, saying that when he finds the tree -- finds Eden -- put the ring on and get the sap, and then when he returns to Spain, she will be his Eve. As he takes the ring, we go back to Tommy for a moment and see him and his tree approaching the nebula.
Back with Tom, he wakes up suddenly and drops the manuscript on the floor. He heads into the bedroom but Izzi has apparently already left for the day. Tom sees a note on the bedside table, reads it, and next we see him in a Mayan museum. He finds Izzi and she shows him some old documents she's looking at that tell the story of how when the First Father -- the guy the Mayans thought created the world -- died, a seed was planted over his body that grew into a tree, so he effectively became one with the tree and lived on through it. Tom listens to this but it's obvious he doesn't really care. He tells Izzi that he's going to bring the car around but as he leaves, she collapses. He runs and catches her, and she is brought to a hospital where Tom and her doctor explain that she had a pretty serious seizure. Before the doctor can explain what they're doing Tom butts in and says that he is going to fix her (presumably with his plant drug). Unfortunately, there is still no change in the tumor on Donovan's brain and he pretty much loses his patience with everyone, even yelling at his boss when she asks him to think of Izzi, saying, "WHY THE F**K DO YOU THINK I'M HERE?!?!" His boss walks out and Tom screams in frustration, knocking everything off his desk and silently weeping. He later goes back to the hospital and sees Lilian there talking with Izzi. Lilian comes out and Tom apologizes for his earlier outburst, and Lilian seems pretty understanding. Tom goes in and Izzi says that she's not afraid of dying anymore. He shows her that he brought her manuscript and she says that she's done with it and wants him to write the last chapter. When he says he doesn't know how it ends, she says that he will know, when it's time. She makes him promise to stay with her all night, and he does, holding her hand as she falls asleep. Eventually, he gets up, picks up the manuscript again, and looks it over some more.
In the bubble, Tommy leans close to the tree and says that they're nearly there now, and asks the tree to hold on just a little while longer while he takes another piece of its bark for breakfast and examines the many rings that cover his arms and legs and chest. In the hospital, Tom wakes up to a beeping and after a few seconds realizes that Izzi's pulse is fading. He presses the emergency button and some doctors come in and take him out while trying to resuscitate Izzi, but they are too late and an agonized Tom watches as they pull the sheet up over her head. He breaks into the door and yanks the sheet down, trying to resuscitate her himself, but eventually he gets pulled off and heads to the window, where he screams in denial. In the jungle, Tomas is outside his groups tent and waiting for Father Avila. For his part, Avila is lining up the stars with the holes in the dagger. He finds the right spot to stand in and looks around for a tree or a pyramid, but finds neither. Suddenly he looks down and sees stone buried beneath the grass. He digs a little and realizes the whole pyramid is buried and as a heavy storm starts, he screams, "WE FOUND IT!!!" Back at camp, Tomas's men are speaking of abandoning their quest and heading home. Just as the priest returns with his news, the men reach their breaking point and strike at the priest. Tomas dispatches all but two of them, who lay down their swords, and is told by the dying priest where the pyramid is...
At a snow-covered farm, we see a funeral for Izzi. Lilian is speaking about how unafraid of death Izzi was when Tom starts walking away. Lilian finishes and runs to catch up asking him where he is going. Tom, obviously very embittered now, tells her that death is nothing more than a disease and he is going to find the cure. That night, we see Tom alone in his and Izzi's bedroom looking at where his ring used to be and holding Izzi's manuscript. He puts it on the table but knocks over a jar of ink that had a pen in it. He curses and sets it upright, then takes the pen and looks at where his ring used to be. He pokes a hole in his skin with it, dips the pen in the ink, and then puts the ink into his blood. Suddenly, all of the anguish rushes in on him and he breaks down. Back in the bubble, Tommy is looking up and sees that they have finally arrived at Xibalba, the dying nebula Izzi once pointed out to him. He tells the tree that they've arrived and soon she will be reborn, and they will live together forever, and that it was her that pulled him through all these long years. Elsewhere, we see Tom marching into the hospital looking determined and dangerous and he basically says that from now on their work is that plant and how it can stop dying, or at least postpone it, although everyone looks at him like he's crazy. Back with Tommy, the tree suddenly starts dying at a massive rate, and Tommy once again cries out in denial over the fact that they were so close. He hugs the tree and says that they were supposed to be together forever when Izzi appears behind him. He asks what she wants and she turns into Isabella, asking if he will take this quest for Spain. He confesses that he doesn't know how to, and Izzi tells him that he does -- he just needs to do it. Nodding, he turns, climbs the tree, and leaps up, leaving his bubble behind and forming a new one that holds only him in a meditative position.
In the Mayan temple, the priest is striking down Tomas when a bright light suddenly flares. In the light, the priest sees Tommy floating serenely, and the priest says, "Forgive me First Father! I did not know it was you!" The priest offers Tommy the dagger Tomas dropped, and Tomas (not Tommy, who is still floating towards the star) picks it up and takes the life of the willing priest. Tomas marches forward and at last finds the Tree of Life, which is more beautiful than he could have imagined. He marches through a shallow rectangular pond to get to it and kneels before it, pulling out the ring as he does. He lays it on the ground and plunges his dagger into the tree and white sap bleeds out, causing flowers to spring up wherever it falls. He takes some of the sap and applies it to his wound, and the cut from the dagger instantly heals. As Tommy drifts farther up and is overtaken by the star, he experiences one last vision of Izzi and says, "I'm not afraid." Izzi puts a ring on his finger and the star finally goes supernova, frying Tommy. Tomas holds his hands out and drinks from the tree, feeling a sense of serenity in doing so. He picks the ring up and moves to put it on when a pain suddenly strikes his chest. He looks at where his wound was and white flowers suddenly bloom from it. He pulls them out only for more to take there place, and soon they are coming out all over his body, ultimately turning him into nothing more than a slight hillock covered in white lillies which is at the base of the tree in the shape of a man. Finally, we see Izzi telling Tom to come and walk in the snow with her. He tells her that he's busy, and she frowns and walks away. He goes after her but is stopped by one of the doctors. He ignores the doctor and heads outside and catches up to her. We see Tom walk up to Izzi's gravesite and plant a seed for a tree above her grave. Finally, we see Izzi lying in bed with Tom leaning close to her and saying, "Don't worry...everything is alright..."
Further explanation comes from JD, "An Intelligent Film Viewer."
When Tommy (the 500 year old Tommy) is about to go towards the supernova in the end of the film, he says he is NOT afraid. The whole point of the movie was that “death” is not a disease like Tommy said, but instead a path to “awe” which keeps being repeated in the movie over and over. When Tommy goes to “die” in the supernova, he realizes he is not afraid of death, just as Izzie was not afraid of death right before she died, because he finally understood her epiphany, that death was only the key to another form of life, or “awe” as they continually call it in the movie.
Tomas and Isabella weren’t Tommy and Izzie in another life. They WERE the exact same people as Tommy and Izze, and as the 500 year old Tommy (who actually has his own name, you read it in the credits but it’s never spoken) and the tree form of Izzie. This is kind of hard to understand because you have to get outside of western thinking and accept that it is possible for them to each be three people simultaneously, because they are outside of the bounds of time. This is because the 500 year old Tommy is able to shift through time because he’s reached another plane of existence through his meditation. That is how he has survived for so long, through the meditative arts we see him practicing again and again.
The spoiler left out a key scene where after Izzie dies from a brain tumor (which is what Tommy was really trying to cure in the monkeys) Tommy finds a seed from a tree that Izzie wanted to point out to him on that walk she was asking him to take in the beginning of the movie. He plants the seed over her grave.
This seed grows into a tree and since it fed off of her, she is, in essence, part of the tree (the tree of life) , which once again reflects how death is the path to “awe”. Izzie herself explains this concept (and we are supposed to understand later how it applys to her) when she is in the museum and talking about how the first father became one with the tree and started the world, and how through his death there was the life of everything and he was also a part of that life.
I know it’s quite difficult to understand, because time loops back on itself in this movie and is cyclical, you just have to accept it in this movie. So modern day Tommy tried to save his wife, planted the tree of life over her grave, made her one with the tree. He was able to manifest himself in Tomas to the Mayan, where he was recognized as being the first father (hence, he’s gotta die from the tree, which he does).
The whole point of this movie is to get away from the idea of the death of the human body, basically death as we know it, as being evil or bad or a disease. Instead it is a gateway to another form of life. So Tomas was simply converted to another form of life. One with the tree, one with everything.
If you’re trying to figure out how all this works out in a linear sense, you probably can’t, because the movie doesn’t occur, and can’t even be arranged well in a linear sense. The events are intertwined. This is symbolized by the ring that Izabella gives to Tomas, the wedding ring which Tommy loses, and in the end, the ring that tree Izzie gives back to the 500 year old Tommy.
Basically, in the end of the movie, Tommy finally becomes enlightened, and realizes that his fate is not to bring Izzie back from the dead, into human life as he may have originally planned, but instead to realize that both he and she are to become one with everything in the universe, and to realize death as a means to awe. This is why he sacrifices himself up to the supernova, simultaneously in Tomas’s time being the first father as he becomes one with the tree.
It wasn’t that Tommy couldn’t “save” Izzie. It’s that he finally realized that Izzie didn’t need saving, and neither did he. They would be together forever, just like he wanted, but in a different way than he thought.