Here is a hypothetical conversation where emphasis on _did_ might make sense:

> **Speaker A:** "You look sweaty.  Were you working out at the gym?"
>
> **Speaker B:** "No, I didn't come from the gym."
>
> **Speaker A:** "Well, where _did_ you come from?"

Speaker A wants to elicit an affirmative statement by that emphasis.  The emphasis also expresses annoyance at Speaker B's uninformative negated response.