[spoilers]
Whenever it flashed back to the past and revealed more of the 'Conquistador' story, it was cued from Izzy's book. It was not an autobiography. Izzy was coming to terms with her mortality and recognized her husbands valiant medical work to try and fix her. Izzy, upon finding she was going to die, attempted to latch onto ANYTHING that'd make her not fear it. She became attached to an ancient myth of the First Father and the tree of life in the Mayan universe. She fell in love with the idea that a whole culture would see their underworld as something that was dying. Death to create. So she began writing a book about Queen Isabelle and the conquistador and their 'quest' to find the Tree of Life. She paralleled it with her life (and inevitable death) and that of her faithful and workaholic husband. The Inquisitor maybe represented something else, like the tumor but maybe just the external threats of personal pursuit.
In the first twelve chapters it told the tale of the Conquistadors success, maybe mirroring the fact that she knew her relentless husband would find a cure but would maybe be too late. This is why at the end of the past the conqistador became consumed and thus couldn't return to the Queen who was being overrun by the Inquisitor. This is also why she couldn't finish the book, because she knew she was going to die and that the remaining story would take place AFTER her death.
That is Izzy.
Thomas, meanwhile, was already feeling guilt at not BEING with his wife as much while trying to find the cure. He was relentless and unscientific, fighting against the clock so to speak. You can tell he 'denied' or tried to, her growing attachment to the myth and the acceptance of death, usually recoiling or crying or whatnot. Anyway, his story takes place in the present and 'future' and is divided accordingly.
So. He fails to save her but does find a cure, too late as we know. He lost his ring, maybe symbolic of the fact he was not with his wife as much as he wish he had been and compensates by tattooing. I think all the lines on his arms in the future are rings of a tree, showing how many years AFTER her death he lived. Again, I don't think the future segment is literal at all but merely a 'vessel' of thought and grief and the attempts to overcome it.
So he does the rings on his arm, solves the cure and probably becomes famous in doing so. He also plants a seed, which is rotted because it was given to him by her so years passed and plants it at her grave. He still feels grief and guilt for many things he didn't do during life and is haunted by her memory. He finishes the novel also realizing to live with her eternally again he must end it. Remember that is the big revelation at the end of the future segment when he detaches and heads towards a dying nebula? To end it. This is where I think he comits suicide.
That is Thomas.
So the whole story is about their relationship in modern times. I imagine the 'future' seqment is all about Hugh Jackman coming to terms with his failure. He has been asked to finish the novel and has also done right by his wife in planting a seed at her grave. He feels guilt, however. This is why the tree in the bubble that represents her also dies before he reaches the Nebula.
Personally I think after he finds the cure and revolutionizes science and also planting the seed, he commits suicide, but this is purely my assumption. To end it was the big revelation I feel was a double entendre to his life as well as the book which undoubtedly he'd get published somewhere after writing the last chapter.
[/spoilers]
I'm a poor, jobless teenager.