In 1506 Leonardo returned to Milan. Many of his most prominent pupils or followers in painting either knew or worked with him in Milan, including , and . At this time he may have commenced a project for an equestrian figure of , the acting of Milan. A wax model survives and, if genuine, is the only extant example of Leonardo's sculpture.
Leonardo returned to Florence, where he rejoined the on 18 October 1503. He spent two years designing and painting a mural of for the Signoria, with Michelangelo designing its companion piece, . In Florence in 1504, he was part of a committee formed to relocate, against the artist's will, Michelangelo's statue of .
Through much of the fourth season, Leonardo becomes increasingly stern with himself and adopts a greatly aggressive personality (which has been likened to Raph's previous impulsive and hotheaded ways on many occasions). Leonardo also shows considerably less reluctance in using violence to interrogate people, and devotes himself to even greater lengths of training. His brothers worry about him and Splinter feels he must move on. It comes to a head when Leonardo loses his temper and nearly causes Splinter serious injury during a training session. Splinter sends Leonardo to find Master Yoshi's own sensei, The Ancient One. Leonardo encounters a strange short man, as well as obstacles that echo his own anger. In the end, Leonardo admits that he was angry over failing his family while fighting the Shredder and that his only option was to self-destruct the ship to stop him. Leonardo comes to terms with his anger, accepting he did every thing in his power, and begins training under the short man, who turns out to be the Ancient One. Leonardo only leaves when he learns that his family is in danger (a result of Karai's vengeance, which destroys the lair and presumably eliminates them). Leonardo returns to the city, reunites his family in a safe location, and battles Karai (giving her one last chance to leave the Turtles in peace).
In the Season 3 episode "Take Me to Your Leader!", Leonardo gives up his leadership and walks away after a dream he believes convinces him he is no longer a good leader. The others have to find him, and stop , , and from draining energy from the with a and store it in solar batteries. However, Leonardo returns when he spots a collapsing due to . After a man says that everybody talks about the weather but nobody does anything, Leonardo realizes his responsibility and begins to search for his brothers. He later finds them, and together they save the .