In Part 7 of the main Personal Story, I chose “dishonored by allies” as my fear, and then went through most of the missions relating to Syska and the mesmer, but then, according to the wiki, the final mission in the chain should be “Delivering Justice”:
http://wiki.guildwars2.com/wiki/Delivering_Justice
where you confront Syska and find out what the deal is with the mesmer. Instead, my final step was “Liberating Apatia”:
http://wiki.guildwars2.com/wiki/Liberating_Apatia
which is supposed to be the end of the “make another suffer” choice. I was thoroughly confused because the game was acting like I should know who the heck Apatia was and what that weird underwater drow with butterfly wings was, and how I had somehow acquired a magic krait orb, but apparently it was just entirely the wrong storyline.