For unknown reasons, Leonardo left his post with Cesare Borgia in 1503. He may have sensed that Borgia's power would soon come to an end, or he may have been disgusted with some of the assassinations that Borgia had performed in recent months.

Back in Florence, Leonardo may have renewed relations with Machiavelli: the Arno River ran from Florence to Pisa, and the two cities were now at war; Machiavelli served as one of the directors of a project to divert the river so as to prevent it from running through Pisa, thus depriving the inhabitants of fresh water, as well as supplied brought by riverboats. Leonardo made many sketches of the river and of the planned new course; most likely the directors also consulted him as an engineer. However, the project itself failed.

By this time, Leonardo had gained an immense reputation, and Florence wanted to take advantage of its famous son: the new, republican government had built a large council hall at the Pallazzo della Signoria, and now commissioned Leonardo to paint the Battle of Anghiari, commemorating a historical Florentine battle, on one of the large side walls.

As with Leonardo's other major mural, the Last Supper, technical problems doomed this painting to failure. It deteriorated very quickly, and the painter abandoned it in 1505, long before it was completed. The only records we have of it are a few of Leonardo's sketches and copies done by other artists, such as this one by Rubens. Rubens's style shows through in the copy; and thus it should not be taken as a completely accurate representation of Leonardo's original. Even though Leonardo often designed machines of war, he often spoke of war's beastliness; he meant the Battle of Anghiari to illustrate its horrors.

Most critics agree that Leonardo began work on the Mona Lisa while he was still in Florence, probably around 1505. The famous debate around the painting's subject has raged for years: recently, some have used computer technology to compare the portrait with Leonardo's own self-portrait and suggest that the Mona Lisa is a female version of Leonardo; other, more reasonable arguments assert that the figure is the wife of Francesco del Gioconda. But if the sitter was not Leonardo himself, she never received the portrait, for when Leonardo finally went to France, he took it with him. After his death, the French Royal Family kept the painting, until the French Revolution, at which point the Louvre was opened to the public and the painting became the property of the French people.

Not only has the Mona Lisa been damaged by darkening layers of dirt and varnish, but it has been practically ruined by its own fame: who today can approach that famous smile with a fresh eye? Yet one gains much from a closer look. First, the head is round and full of flesh, in contrast to the flat, misshapen head of the Portrait of Ginevra de Benci of 1474. Leonardo's painterly career can be described as a quest for the perfect female head. The Mona Lisa is also relatively mute in its coloration–that is, its light coloring is due not only to fading, but due somewhat to the artist's intentions. Leonardo's preference for the shadows, veils, and sfumato possible in oil painting reaches its culmination in this portrait, where color and light are in perfect subservience to volume. The background here is typical of Leonardo's work: rocky crags and mists.

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