There's plenty for PVE'ers to do in the eng-game, but to be honest, little point in doing it, at the moment.
Sure, I can run endless missions on Challenge / Heroic for that random drop but it becomes stale very quickly. RNG is a cruel mistress!
I think your agent should be given a series of special under-cover missions, where they would have to infiltrate each Faction in turn. Once "on the inside", they would be given missions / dailies from that current faction to carry out hostile activities against other (non-division) factions. Could be simple things like taking over a Control Point, or killing a named boss or capturing Supply Convoys.
For this you would gain faction points, which can be used to unlock special high end weapons and mods from vendors of the current faction you're working with. These would be of similar calibre to those Exotics that we all seem to love so much.
Grinding differnt faction points seems to work very well in other games but doesn't have to be mandetory, so that players who don't want to do it, dont miss out. But it does encourage extended gameplay where some players might just give up on the game until the next major update without something like this to "keep them busy".
Just an idea.