This one's fairly cheesy, but what the heck:
Q: I'm trying to kill off an enemy agent, but my own agents can't seem to touch him no matter how good they are. Is there anything else I can do to get rid of him?
A: If you're absolutely desperate to remove an enemy agent from the campaign map (and your assassins/other agents aren't having any luck), there is an exploit you can use: Surround the enemy agent with army units, then have an additional unit occupy the same space as the enemy agent; the agent will simply disappear and not return.
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