Just from playing, there seems to be some sort of a map you can gather. I assume that you fight the bosses as normal to gain the broken parts of the jewel, and judging from the spaces you can update your weapons.
Looking at the cinemas and using the dubious power of Babelfish, it seems that the game has two endings. I'm guessing it has something to do with giving up the jewel to the proper owner, but I'm probably wrong. Also, the cut scene images seem to be of badly mutated people under odd lighting. Reiko and Yuko's images are particularly odd since they're not centered on the screen like the mutated weird ones. I suppose that adds to a sense of drama. And makes the images smaller.
Still - interesting.
Also - the page below has information about opening the music test and the like.