Was the story of the Conquistador and Queen Isabella real or just part of the story Izzy wrote?
It seems that Izzy was somehow remembering her previous life and writing it as a fictional novel. It is proven that this did happen when the Mayan king mistakes the Conquistador as First Father when Tom from 2500 appears before him as the Conquistador. At the time he seems to be living as his future self in all of his lifetimes. Tom in 2500 does say in the beginning of the movie that he trusts Izzy, who at the time the tree and appearing to him as her old selves. He says she is taking him through time, and we witness that as the movie, so she is taking him back to his previous life as the conquistador and Tom as the doctor in 2000. Tom is also visited by Izzy in her two lives, as Izzy from 2000 and Queen Isabella from 1500, further evidence that it all really did happen.