Since I just added disasters to the game I'm working on, I went ahead and added something similar. Here's an attempt at adding tornadoes to Minecraft:
It kind of looks like one ... It's really just a bunch of explosions that go off each second. There are also different sizes of tornado, damage, life time, etc.
I divided it up into three parts:
A Tornado class -- this is just a normal class that holds the information like location. It also has the code to spawn the explosions and update its remaining lifetime.
TornadoUpdater -- Tracks all of the tornadoes in the game and updates their states, removing them if they've "died."
TornadoMod -- serves as an entry point.
Right now it just spawns vi a command, but I Hope to get them spawning during thunder storms at some point...