There was no storm. The submarine submerged for a routine exercise and something went wrong. If it went below crush depth and imploded then some debris could make it to the surface. If it suffered an internal explosion, ala the Kursk, then debris could also have reached the surface.
How does sinking an Indonesian submarine help China rule the world?
Note: I didn't say definitively that China sank it, just said I would bet that China sank it.