Troops are In Japan Now?

According to an article on MSNBC.COM, Hilary Clinton went to Japan to try and "reduce tension" from our troops being there.. North Korea even threatened a missile launch! First off I don't know why our troops are there in the first place.. I understood they were only in Afghanistan and what not to keep the peace because no one was governing them? Clinton went there to warn them telling them that if they did launch the missiles there would be no way in fixing the relationship between North Korea and the US. I'm still trying to figure out why our troops are there and they want to launch missiles. Majoring in international business... I could be over there doing exactly what she is. It is scary to know that while I'm just living my life, the US is getting threatened by missiles. Wasn't the war supposed to be over or trying to be ended when Obama came to office? The world is a complete mystery to me