It was suggested that the motive of the murder was the brothers' rivalry in the affection of Donna Sancha, wife of Giuffre, the pope's youngest son, while there were yet darker hints at incestuous relations of Cesare and the duke with their sister Lucrezia.
The connexion began in 1470, and she bore him many children whom he openly acknowledged as his own: Giovanni, afterwards duke of Gandia (born 1474), Cesare (born 1476), Lucrezia (born 1480), and Goffredo or Giuffre (born 1481 or 1482).
Cesare, then a youth of sixteen and a student at Pisa, was made archbishop of Valencia, his nephew Giovanni received a cardinal's hat, and for the duke of Gandia and Giuffre the pope proposed to carve fiefs out of the papal states and the kingdom of Naples.
But through the intervention of the Spanish ambassador he made peace with Naples in July 1493 and also with the Orsini; the peace was cemented by a marriage between the pope's son Giuffre and Dona Sancha, Ferdinand's grand-daughter.
His goods were confiscated, his aged mother turned into the street and numbers of other members of the clan in Rome were arrested, while Giuffre Borgia led an expedition into the Campagna and seized their castles.
Cesare then returned to Rome, where his father wished him to assist Giuffre in reducing the last Orsini strongholds; this for some reason he was unwilling to do, much to Alexander's annoyance, but he eventually marched out, captured Ceri and made peace with Giulio Orsini, who surrendered Bracciano.