Good ideas!
The original Trek was often a political or social metaphor - and the War on Terror would have been the kind of subject it dealt with. My Movie-era game had Orion nationalist terrorists (FASA Orions were half in Federation territory), as well as Klingon and Romulan agents provocateur. The climax involved an attack on the UFP's presidential vessel during a goodwill tour.
Throw in the aftermath of a supernova in the affected area, and you'd get a good parallel to some of today's events.
Jon
"There are worlds out there where the sky is burning, where the sea is asleep and the rivers dream; people made of smoke and cities made of song.
Somewhere there's danger, somewhere there's injustice, and somewhere else the tea is getting cold. Come on, Ace, we've got work to do."
THE DOCTOR, "Survival" (Doctor Who)