My explanation's too simplistic, but I don't want to overthink this story. I think that the Isabella/conquistador parts were Izzy's story, which Hugh Jackman (I can't remember the character's name) completed after her death. The scene in which the conquistador became fertilizer was Hugh's acceptance of his own death. The one part that confused me was the seed. Was it, in fact, the tree of life? I have no idea.
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