I aborted a campaign in which the protagonist signs on with the NTF some time ago ... it was more of a prologue to another project and meant to flesh out the character before she re-appears in the main campaign but I think it still qualifies.
I uploaded the dump for that campaign to FSMods and you can check it out (
Download at FSMods); it deals mostly with the end of the Rebellion and the escape to and through the Knossos I...
The missions in the dump are all alphas but they should work in a fashion without you having to mess with them, just usually "access via techroom" instead of being a campaign - all unfinished missions are missing though, so there are a huge story gaps
which deal tie together some story threads about the GTVI and NTF and the importance of the main character of the story to individuals in both factions