Well, to put it simply, you wake up in the middle of a cave with no recollation of who you are or why you're there. After stealing a weak gun and falling into a town, you disocver that an evil doctor has been kidnapped citizens of the town- called mimiga- and feeding trhem red flowers, causing them to mutate and become monstrous.
Outside of the plot -there's a lot more to it than that- it plays like Metroid, has wonderful music, and has a charming pixelated look to it.
If you want to try it out Cave Story 3D comes out in November for the 3Ds, or Cave Story itself is on the Wii(which I don't reccomend) for 1200 points, the DSiware for 9.99, and free to download on the computer.