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Wouldn't it be correctly called a "megatonne", as SI prefixes aren't typically applied to imperial units?

For some reason, people write megaton and mean a metric megaton. Megaton as a TNT-equivalent also refers to a metric tonne.

But (Sid Meier's Alpha Centauri) is an American game and it could actually refer to a non-metric megaton

I believe the world portrayed used metric, though. They at least talk about nano-meters and etc in their blurbs.