Possibly too silly to use but you could extend the temporal time war story thread of Enterprise into the TMP and have Suliban sabotage be the real reason behind the many glitches in this important mission.

I hated the way that strand of the series was just dropped when they were trying to salvage it.

What is it with Sci-Fi show writers and Time Wars that go nowhere?

It would add a bit of a twist if mystery man turned out to be Will Decker/V'ger or even Nero having survived his encounter with what they used to call a Black Hole.