Did the Rogue arc.
With respect, your writing is significantly better than your sense of game balance. I don't feel it is very reasonable to expect a lvl 25-29 character to solo a roomful of Legacy Chain (including a boss) all at once, especially since it wasn't actually the climatic fight - to clarify, I had set my difficulty at +0/x1. Now, I ran the arc with my only rogue toon, which happened to be an exemplar'ed lvl 50 TW/Bio scrapper with a billion inf IO build, so I just AoE'ed them all to bits while their rocks whiffed (Because of this, I may have missed how difficult it might have been to defeat the actual final boss, or the large number of PPD mobs in the earlier mission). However, if I had gone in with a squishy defender I suspect I would be cursing at you right now. Please do consider allowing the spawn system to handle mob balance, flawed as it may be.
On the other hand, I liked the writing very much. Conversations were extremely amusing, especially regarding the Warrior boss's "family vacation" and the entire thing with the Family boss. The moral dilemma is a little cliche, but as with most CoX arcs the story is really all about the NPCs (in this case the final boss), not the player. From that perspective, it's significantly more interesting. I do however approve of the "in-between" moral options at the end, where you get something for your "mercy" - too often, moral choices in video games are binary, lack nuance, and ridiculous - the most egregious example of which I can recall is "Cure the little girl vs Murder the little girl" in Bioshock. I am very happy that my greedy rogue can try to weasel her way into a payoff while sating her conscience.
Incidentally, I did the arc twice, taking the same end choice, because it was clear that an action I chose in an earlier mission changed the response of the final boss. This is fantastic, in my opinion, because it is a very good use of branching options that can convey a sense of consequence for earlier actions, something that gives me a lot of hope for future stories.
Lastly, and this is a little off topic, but I do hope that future arcs that involve actual Villains won't solely be driven by a mere profit motive - this is perfectly fine for Rogues (in this case), but it annoyed me to no end that the vanilla CoV arcs were almost entirely about scoring some cash. CoX in general also suffers from having most stories feel rather impersonal for the player - we stumble into someone else's tragedy/stuggle/story and go in to meddle, and none of the stories are really about us. The signature story arcs started to go against this trend (at least redside), and I would like to see more of that sort of story.