Don't de-ally the existing EVO governments! If players begin the game with the plug already in place, they'll have some unexpected results in terms of the way the governments interact. You don't want them to "de-ally" until the plot gives them a reason to do so!
A much better way is to create new duplicate governments, systs, and spobs, whose only difference is not being allied (plus whatever other changes you want to make, of course.) Then, when the plot reaches that point, use a mission bit to instantly swap out all of the affected systems. It's a bit trickier to program, but it works much better in the long run!
Glenn
PS: A common mistake using visbits, which is reasonably easy to avoid, is this: NEVER switch the visibility of a system the player currently occupies. It makes some strange effects, and gives a very amateurish feel to things. Always have some reason to keep the player away from the affected area at the time of the change!
PPS: The Miranu and the Zachit splitting up?! Sounds cool! I'd love to know why they do so, but I guess I'll have to wait for your plug to come out! Best of luck! 
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If a little knowledge is dangerous, where is the man who has so much as to be out of danger? - T.H. Huxley
