I do have a "WHERE" clause, but that is not of much help. If there are no errors in the database then each story MUST have a corresponding thread. The only thing that will actually limit the number of returned rows is a "LIMIT clause".
No, that is not how queries work. They use where to optimise. the explain will clearly show you this.
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I am using an index, but I do not agree with your conclusions.
They are not conclusions, they are facts. Use explain once or twice, and all will become clear.