Think Galactus from the comics. http://en.wikipedia.org/wiki/Galactus Or perhaps the Borg, etc. A being/race that everyone fears to deal with.
Upon his eventual defeat, perhaps a significant event can take place that will change the game dramatically for the players/alliance that does the most damage.
I think it would also be good if he occasionally takes a little from different players in the game as an incentive to attack him. No one should have to fight him if they want, but if they desire to take out the super being, the entire alliance must declare war on him which will incur greater losses from him. (But allow them to attack him)
This is kind of on a whim, im sure you guys could expound on this idea much more.
Edit: On another note, this would provide a very interesting counterweight against ridiculously powerful alliances. You have to choose careful when to take on the superbeing, because while you are embroiled in battle with him, another alliance could decide to use that moment to start massing you!


