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The planet Rajatha Prime featured a unique ionosphere which prevented accurate sensor scans being taken from orbit, because of this the ruins of a Rajathan city remained undiscovered on the planet for some two millennia. (TNG comic: "Captain's Pleasure")
In 2375, during the final battle of the Dominion War, the USS Defiant fired its weapons on a Breen battlecruiser that had entered the ionosphere of Cardassia. (DS9 novelization: What You Leave Behind)