Bosch's intentions are made very clear through his monologues and through Petrarch's later command briefings.
One thing bothers me though- couldn't Bosch just been a good little admiral and, with his followers, simply get everything he wanted SILENTLY and PEACEFULLY ?
GTVA "buried" the GTI's research, they certainly wouldn't let Bosch do anything silently and peacefully.
Bosch needed a "smokescreen," IE the NTF's campaign of genocide, to give him access to Deneb and elsewhere for purposes of archeology. Apparently, his "plundering of [Ancient relics]" gave him the location of one of the Ancient's Knossos portals, and the Trinity defected from behind enemy lines and activated the portal on Bosch's command.
With his smokescreen disippating in the face of the Collosus and with the ETAK project operational, the NTF became unneccessary. Bosch ordered a Hail Mary to the Knossos, and used his NTF-sheep as flak shields to protect the Iceni and the ETAK project.
The real question is what happens next.