Complex sentence: A ballistic missile is only guided during the relatively brief initial powered phase of flight, whose trajectory is subsequently governed by the laws of classical mechanics, in contrast (for example) to a cruise missile which is aerodynamically guided in powered flight.
Split into simpler sentences: A ballistic missile is only guided during the relatively brief periods of flight, and whose trajectory is largely un-powered and subsequently governed by the laws of classical mechanics. This contrasts to a cruise missile which is aerodynamically guided in powered flight.