So, long story short, I want to have 100% control of the Mediterranean by the end of the game, but maintaining contol while playing through the story would become a full time job.

Without explaining more than the cliffnotes of the plot (I haven't finished yet, so I'm steamrolling through it to be done before AC3 comes out), can anyone let me know what the last mission before you can no longer do mediterranean defense missions are? My plan is to just stop before the final mission, grind out control over all the cities, THEN go on to the final mission.