When someone navigates a ship or an aircraft somewhere, they decide which course to follow and steer it there. You can also say that a ship or an aircraft navigates somewhere. He was responsible for safely navigating his ship without accident.
navigate (third-person singular simple present navigates, present participle navigating, simple past and past participle navigated) (transitive) To plan, control and record the position and course of a vehicle, ship, aircraft, etc., on a journey; to follow a planned course.
He is navigating a transport ship coming in to land on Mars. The Elbe River is not as easy to navigate as the Rhine. They navigate by the stars and by the lie of the land. Some birds fly at night and navigate by the stars. In times past we Rabari navigated entirely by the stars.