Agitate means to stir up. If you watch a horror movie at bedtime, you may be too agitated to sleep. Movies like that can agitate all sorts of adrenaline responses in the body.
Agitate derives from a Latin word that means "to drive away." The meaning has changed, but you can see where old meets new—a washing machine agitates dirty clothes in warm soapy water to drive away the dirt. You agitate or shake up salad dressing to mix it, driving the oil away into the vinegar.