A scientist made slave to a government UFO reverse engineering project must escape before the ones who created the craft come back to get what is theirs.

Maybe try making the discovery of the aliens immanent return the inciting incident. This would clarify the start of the story.

Good suggestion about the rogue General strait away puts images from 'Doctor Strange Love' and 'Apocalypse Now' in my mind that really helps picture the added stakes.

What exactly is a Reverse UFO engineering project?

"After he's conscripted by a rogue General to reverse engineer a crashed UFO, an absentminded scientist must escape before the aliens come back to get that's theirs."

How does the scientist no the aliens are coming?