I just saw The Fountain recently, I was truly amazed at the art direction of the film, it was simply astounding. The narrative was a bit harder than it needed to be to ascertain but is highly rewarding.
*SPOILERS*
For instance, it took me awhile to figure out how the 3 storylines worked with each other. At first I though the Imperial Spanish past was simply Izzie's book, the present was the main narrative and the future with the Treeship was the internal battle Tomas' character was facing having to deal with Izzie's impending death.
As it turns out, the future in which Tomas appears as a monk within a bubble Treeship ascending the stars to the Xibalba (sp?) Nebula is the film's 'present' timeframe. The flashes back to when he was a surgeon and before Izzie died was the past that haunted him. I was right, however, about Izzie's novel it was simply a book she wrote to display her feelings about life and death to Tommy so that he could let her go. That is why she wanted him to finish the last chapter. Hence, when Tomas in the future finally realizes that death is not the end, and accepts her death (and ultimately his as well) he metaphorically finishes the book. Thus, we see future Tomas collide with the Tomas from her novel in a flashback showcasing his final understanding of life by accepting death (the flowers devouring him after he drinks the sap, the allusion to which Izzie hinted at earlier: death as a form of creation or rebirth).
As I said before the film could have been assembled better so that its timelines were more easily digestible, but it is still a great film as it stands.
I also saw Children of Men too, another top notch film. Highly recommended.