[1] Cesare Borgia's biographer Rafael Sabatini says that the truth is fairly clear: Alexander fathered the child with an unknown Roman woman.
Pope Alexander VI issued two papal bulls, both dated to 1 September 1501, assigning different fathers to Giovanni Borgia.
The second declared Giovanni Borgia instead to be the son of Pope Alexander VI himself and runs: "Since you bear this deficiency not from the said duke, but from us and the said woman, which we for good reasons did not desire to express in the preceding writing".
The pope was forbidden by canon law to publicly recognize children and did not wish that Giovanni Borgia should suffer in his inheritance as a consequence.
To flee the life Cesare is grooming him for, Giovanni runs away to join Francesco Vecellio, Calderon's understudy, in the Assassin Order.