Often story ideas come from literary influences: an author reads something a play by Shakespeare, a passage in the Bible, a Superman comic that triggers the thought, "Hey, that gives me an idea for a
different story!"
Other ideas come from nonfiction. Pursue your interests! If you like science, try reading popular magazines like Discover, Science News, and Astronomy both for story ideas and because they'll help develop your general understanding of science and keep you abreast of the latest research.
Some stories are old stories retold. The story of Beauty and the Beast, for instance, has been told in countless variations, ranging from Robin McKinley's Beauty to Disney's animated movie.