The same Empire that is probably going to disband your organization for

I doubt it, depends how safe you want to feel?

The only reason they pulled it off, was because the dragonborn was among their ranks.

if it is included in the lore thingy. the dragonborn wont be the one to do it.

This

House Redoran is currently the de-facto ruler of Morrowind as they have a standing army, and repelled the Argonian invasion. They hate the Empire.

Of course, this would change if House Hlaalu were able to overthrow Redoran. But it seems unlikely due to their current state.

Yeah, probably not. But then, it's not like you the player have any control over a faction. It's just a story that you have to play out until it ends and if you don't like the plot tough.

Still doesn't change the fact that you and your comrades failed to protect him.

Maybe in your game. In mine, those foul assassins are now laying in a pool of their own blood. The assassins have been assassinated!

Except, some of the Brotherhood still survives...

"duh duh duh" The plot thickens.

Well it's usually canon that the DB questline is completed in their favor as evident by some of the dialogue

gives in Skyrim.

Cyrodiil: I will also replace your culture and customs, and force you to adhere to ours. Got any leaders of your own? We will replace them with leaders that have our interests at heart, and any traditional election you may have will be rigged to our favor. You will obey all of OUR laws and all of OUR customs. Sway from this, and we will crush you. Capice?

Indeed. They are still dead though.

As if the Cyrodillics were ever capable of crushing anyone in the first place. "Hey let the Orcs, Redguards and Nords do it, while we sit back and enjoy the Colovian sunrise! "

What I'm saying is that in the next TES game Bethesda would most likely go with the route that you guys failed.

I see, it looks like Empire is like any mafia organisation - you will love us (and pay us for protection) or we will slaughter you...