Except this isn't really about fraud, is it? Isn't more about whether they should qualify for the tax exemption?
Yes, these are separate (if not unrelated) issues.
You correctly characterized the differences between nonprofits above $200K and below $200K. Some nonprofits, particularly one-person passion projects with an executive director but no staff, purposefully keep revenue under $200K to prevent greater scrutiny. In many cases, it's because these nonprofits have terrible bookkeeping practices. In a few cases, it's because they've spent the money in a way that would raise questions. In Alec's case, I suspect it would be both (if he bamboozled the IRS into providing Axanar an exemption).
I would kill to see an Axanar Productions 990, though... especially the accomplishments section.
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