The best defense against spies destroying improvements is workers. If you can rebuild the improvement quickly, he's spending EPs without getting much return for them. The more he spends, the more expensive his missions become (due to the EP ratio tilting in your favor), and the fewer he can carry out. For key resources, placing a unit on the tile reduces the spy's chances of success. I only do that when I'm at peace and have the units to spare, though. Especially later in the game, I'd rather divert some workers from building useless railroads or idling in my cities and just rebuild in 1-2 turns.
To find out who's doing it, just monitor the EPs. I keep a notepad on my desk where I can periodically check the ratios and jot down my opponents' EP totals. That not only gives me a direct check if something happens that turn, but lets me estimate how many EPs per turn are being dedicated to me, which in turn lets me know if somebody has ramped up their espionage and gives me a good idea of who just hit me when I haven't done a check in a few turns. Of course, sometimes you gain city visibility or another passive effect as a result of his EPs dropping, which lowers the threshold for you. If you get hit with an expensive mission and gain visibility on several cities of a civ in the same turn, he's probably the culprit.
To find out who's doing it, just monitor the EPs. I keep a notepad on my desk where I can periodically check the ratios and jot down my opponents' EP totals. That not only gives me a direct check if something happens that turn, but lets me estimate how many EPs per turn are being dedicated to me, which in turn lets me know if somebody has ramped up their espionage and gives me a good idea of who just hit me when I haven't done a check in a few turns. Of course, sometimes you gain city visibility or another passive effect as a result of his EPs dropping, which lowers the threshold for you. If you get hit with an expensive mission and gain visibility on several cities of a civ in the same turn, he's probably the culprit.
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