grammar - How to ask "Where are you going?" when event already passed?

I'm up-voting Barrie's answer, which certainly is correct. This is more to cover the question in the comments as to when you might use the others.

First, as Barrie said, the most normal way of asking about a past event, is the simple past:

Where did you go?

A response in the simple past might be:

I went to my favourite restaurant.

The present perfect is used to refer to a past event that has consequences in the present. So if you were out with your friend, and then couldn't see them, you might phone them and ask:

Where have you gone?

They've gone somewhere, and that is still affecting things now.

You wouldn't normally use it in response (more likely would be the simple past to indicate where they went, or the simple present to indicate where they are). You might though use go in the present perfect if you left a note:

I have gone to the shops. Back in 10 minutes.

The past perfect is used when we're already talking about the past, and want to talk about something that happened further in the past that had an effect on that point. So you would need a context that was already in the past:

"I was out for a meal last night and I ran into Alice."

"Where had you gone?"

The context is the past point when they met Alice, and the question is about something further in the past that was in effect at that point.

The response could quite likely be in the past perfect too:

I'd gone to that new Japanese place.

It could also be in the simple past, changing the point in the past that is the context of what is spoken about.