So when a user runs a particular report, the pop up appears, and they have to click ok to see the report
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This is not possibe AFAIK. There is not much customization that can be done if you use the default report tab.
The workaround would be to use a custom link for the report, which would direct users to a page (VF, static html, etc.), that contains the javascript for the popup, and a link to that report. But, even with that, someone accessing the report directly from the reports tab wouldn't get the pop up.
If you want to cover 100% of the scenarios, you'll need to create a custom report (outside the reports folder) using a visual force page. This might get tricky if you also need Excel exporting capabilities, but this is the only way I am aware of that would allow you to do this.
