Like most people one of the main things I like about 40k is the background, and the reason I choose my armies is because I pretty much like playing make-believe that I'm the general of a bunch of space army men
So I picked Guard because I like being the good guys, and I also have some sisters. I like the idea of being mere humans in the crazy universe and all that. Thing is my friend I play with has a huge Ultramarines army because he likes being the good guys too (apparently even more than I do). This hasn't really been a problem much before, we've just ignored the narrative element, but there comes a point where you get kind of sick of "training exercises", and neither of us wants to be the bad guy all the time.
I was thinking of creating a narrative that can explain all our battles while allowing both of our armies to be heroic, something like this:
"Blah World was the epicentre of a full scale chaos incursion that was brought under control by the combined might of an imperial guard army group and the forces of the Ultramarines. After the incursion was contained Inquisitor Blah discovered that the taint had infected the whole elite of the planet. The Ultramarines executed the governor and smashed the ruling families. The navy blockaded the planet and then the Ultramarines began the sad task of cleansing the world.
Unfortunately for them, Cardinal Blah has refused to surrender to justice. He has persuaded the pious High Commander of the remnants of the IG that the marines have fallen into heresy, and has inspired the local sororitas convent to defend the faith. The remaining guard elements and the sororitas, believing the Ultramarines heretics, are not going to just lay down and die..."
I think this is pretty good. We can fight each other, my guys get to be the underdogs and my mate's guys get to be the shining knights defending the Imperium. Both think they are working for the Emperor against traitors, and Cardinal Blah may be tainted by Chaos or he could just not want to be stomped on by big blue boots.
How does your group justify imperial versus imperial battles, or the problem of too many good guys in general? At least the Imperium is a towering bureacracy full of human weakness, I'd hate to try and justify why two Eldar craftworlds or Tau septs would fight each other without one of them obviously being the bad guy.