To evacuate is to flee, like how people leave an area when a hurricane is coming. It also means to empty something completely.
If you have to evacuate your home, something horrible is probably happening, like a natural disaster. People evacuate when something like a tornado or act of terrorism makes their homes unsafe. To evacuate also means to empty completely, in the bathroom-oriented sense of evacuating (emptying) your bowels. Similarly, if a chemist empties and therefore creates a vacuum in a flask, she has evacuated the flask. When you evacuate, you clear out.