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In 1478, the Pazzi conspiracy failed to destroy the Medici family and its rule over Florence. However, the suppression of the conspiracy did not end problems for the Medici. In fact, the Pope (Sixtus IV), who was involved in the conspiracy, and Girolamo Riario, from a prominent family from Savona and nephew to the Pope, became involved in a conflict with Florenceas they attempted to oust the family from power. The conflict took place over the early 1480s, with the Kingdom of Naples initially allied with the Riario and the Pope. The war put great strain on Florence, as it was outnumbered and the Pope had excommunicated Lorenzo and the entire government of Florence. One important sub-plot was Lorenzo taking in his brother's (Giuliano) child (Giulio), who was an illegitimate childof the assassinated Giuliano (killed in Season 2). This would prove successful for the family, as Giulio would go on to be Pope Clement VIII, who helped advance the family's interests man year many years later. In the meantime, the conflict took a turn for the better for the Medici's after Lorenzo went to Naples to make peace with the ruler (Ferdinand I) and became his prisoner. He was able to successful successfully get Naples to drop their war efforts with the Riario, thereby weakening Riario's position. The war effort against Florence began to then collapse and Riario was then murdered in 1488, although the series depicts Lorenzo as killing Riario when in fact it was a rival family (House of Orsi)after his war efforts led to financial problems for the city of Forlì. While the war was raging, Lorenzo also began to show a more dictatorial side, as he dissolved the traditional council of Florence and established a council of ten, who were mainly his loyalists. The Medici bank during this time did become over-extended and was running out of funding. As Lorenzo led Florence, he neglected the Bank's finances. His mother was shown as running the bank, but she was taking money from Florence itself, which would later haunt the Medici family.

After the war with Riario, peace did settle in Florence, but new developments created problems for the family. A new friar, Girolamo Savonarola, who was initially supported by Lorenzo, became an important religious leader with a large following. He began to see the corruption of the Medici and, after Tommaso Peruzzi's death who was killed because he began to see the Medici likely took money from the city treasury, things took a turn for the worse for the family. Clarice Orsini, the wife of Lorenzo, died in 1488, while Lorenzo's health began to fail. Lorenzo did see that he needed to invest in the future of his family, mainly in its political interests and influence in Rome through the Papacy. He placed Giovanni de' Medici, the future Pope Leo X, and Giulio in Rome. His daughter Maddalena de' Medici was also betrothed to Franceschetto Cybo, who was a son of Pope Innocent VIII. This helped her brother Giovanni become a cardinal, despite being very young and with little experience. Meanwhile, Lorenzo was trying to get his son Piero more experienced experience so he could rule Florence in the future, but he was shown as less like his father and seemed to be deeply affected by the corruption and killing of Tomasso. Lorenzo's health continued to get worse and after a conspiracy to assassinate Girolamo, Lorenzo was shown as repentant for his family's sins. Historically, Lorenzo died in 1492, with his son Piero soon taking the leadership role in Florence, although that did not last long and the Medici family was ousted and banished from Florence in 1494-1512. In fact, it was Pope Leo X, who was Giovanni Medici, that enabled the family to come back and rule Florence again. The ousting of the Medici in 1494 led to the infamous Bonfire of the Vanities in 1497, which was the destruction of works of art, books, and even personal items deemed to tempt people to sin. Girolamo led this destruction, who himself was executed by hanging and fire in 1498 as he took religious reform too far for many Florentines.