At Assos Hermeias had succeeded in forming his own intellectual circle consisting largely of former Academy members. Thus Aristotle was able to retreat to another flourishing intellectual domain, and around this time he began to formulate ideas that would be extrapolated in his Politics. He also wrote the now lost work On Kingship, in which he stresses that not only is it unnecessary for a king to be a philosopher, which Plato concurred with, but that it is undesirable for a king to be one. Rather, a king should turn the wisdom of true philosophers into good deeds, allowing the philosopher to remain independent.

Aristotle spent about three years in Assos before moving to the nearby island of Lesbos. Settling in the capital city of Mytilene, he shifted the focus of his research to biology. At that time biology as a science was looked down upon and not given much serious attention. Thus Aristotle felt obliged to justify his attention. To do so, he used an innovative teleological approach. Such an approach involves the determination of the natural ends of things, and in the case of biology, the ends of plants and animals. Teleology would provide the basis for many of Aristotle's treatises in other areas, including politics and ethics. More will be said of his biology in a later section.

In 343 B.C., Aristotle was invited by Philip of Macedonia to tutor his son, Alexander. At this time Aristotle was far from the acclaimed intellectual leader of Greece, and Philip's decision probably was based on more practical reasons–Aristotle's connection to Macedonia through his father's position as court physician may have played a role, but perhaps most important was the diplomatic link that Aristotle provided between Philip and Aristotle's friend Hermeias. Hermeias played an essential part in Philip's plans to invade Persia. But shortly after Aristotle accepted the tutoring position, Hermeias was captured by a Persian general and tortured. Hermeias never gave in to betray his allies, however: his final words were, "Tell my friends and companions that I have done nothing weak or unworthy of philosophy." His death moved Aristotle deeply, and Aristotle himself wrote the epigraph that remains at Hermeias's memorial today.

Aristotle served as Alexander's tutor for three years. The education was for the most part formal, consisting of standard subjects such as poetry and rhetoric. Homer constituted a significant segment of their curriculum, as Aristotle attempted to inspire his pupil with the model of the Greek hero. At the same time, Aristotle encouraged the young prince in his hopes for Persian conquest. Aristotle's hatred for the Persians was of course aggravated by the death of Hermeias, and he succeeded in fueling Alexander's already strong anti-Persian sentiments. For Aristotle there was never any doubt that Greece deserved to rule over other nations, for such foreign nations were barbaric and fit for enslavement. Aristotle's lasting influence on Alexander may have been negligible, however. It was on the issue of non-Greeks that student and teacher would ultimately disagree, though the Persian invasion was long underway before Alexander began attempts to unite his two empires in equality.

After Philip's death, Alexander would win Aristotle's favor by restoring his home of Stagira, which Philip had pillaged years before. Nevertheless, their relationship would deteriorate, perhaps culminating in the execution of Aristotle's nephew Callisthenes. Callisthenes had served as the official historian of the Persian expedition, but while he fulfilled his role by writing as he was told, Callisthenes shared his Aristotle's attitude toward the Persians and opposed Alexander on strongly held ideological convictions. Alexander soon had him arrested and executed on dubious treason charges, and Callisthenes died a martyr. It is possible that Alexander even plotted against the life of Aristotle, but he never had the chance to follow through.

When Philip was murdered in 336 B.C. and when Alexander proceeded to crush resistance in Greece, Aristotle returned to Athens. His friend Xenocrates took over the Academy, and Aristotle set up a rival school at the Lyceum. Here he would flourish and produce most of the works that survived to this point, many of which are largely based on the lectures he delivered there. Members of the Lyceum would become known as Peripatetics, named after the area of the school where Aristotle gave many of his informal lectures.