One of the editors I work with was having trouble with punctuation and parentheses (she’s new and young). I had fun coming up with this explanation.
The rule is that if the complete sentence (quote or not) that's in parens is totally within another sentence, then the period goes outside the parens, but if the complete sentence (quote or not) is not within another sentence, then the period goes inside the parens. Take this example:
Her instructions for raising animals are brisk (“Try to remain businesslike—they are not your pets").
The quote in parens belongs within the sentence because it's illustrating the point of the sentence, so the period belongs to the sentence as a whole, not to the quote in parens. (Parenthetically, if the sentence or quote functions like an aside, as this sentence is doing outside of the preceding sentence, the period goes inside the parens.)
Further complicating matters, if the quote or sentence within parens is a question or exclamation, that punctuation would go inside the parens (like so! and is that clear?). And you see the period for the sentence as a whole still goes outside the parens. (Is this clear? And does it make some sort of sense?)
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