Fortifications Besiege Command is only 10% Chance to Destroy

However, if you have ANY 2 ships on top of them at the END of the turn, they will be automatically destroyed Ur Quan Dreadnought can do this by itself (end of turn, its own Besiege Command is bad as anyone elses)

Mission 5 (The Art of War), ends for killing the Starbase instead of of a total map clear This applies to both sides, and in some cases the starting ships won't even be on top of the AI's starbase.

Mission 7 (Exterminate) can be won by the Hierarchy player for killing all Colonies as an alternative to killing all Ships+Starbase (the AI will build more, so its more something to keep in mind when playing on Alliance side as something the computer might do while avoiding fighting you)

Mission 8 (Proving Ground) can be won by the Hierarchy player for killing all Mines. (again not normally a good idea for human to try, but keep in mind when playing as Alliance against an AI who never tries to move into your stuff)