Okay mega-late reply but the servers were having problems when I tried to reply originally and then I just forgot.
I think you have hit the nail on the head here. We do seem to be largely advocating the same approach. Let the DM come up with the framework of the story but listen to the players and let them shape the story and fill in the details. I also agree with you on the issue of providing access to Sigil, its pretty easy to keep the PCs out if that's your intent, was just using the previous example.
As for Perkins, what I think he was doing was merely trying to get them back onto the particular story line. The line in his graphics represented the general story line rather than the actual actions of the players. To me, the most telling part in this regard was his comment that the players haven't questioned the new NPC yet, but if he's patient, he's confident they will. If he really wanted to force them back onto a predetermined path, he would have simply had the new NPC "info dump" on them when they met her. This not only would have been fairly heavy-handed, it also would have been a break from the verisimilitude of the organization in question.
To pull an example from my own campaign, the PCs were thrown forward in time at the end of heroic tier. They had a chance to prevent this, but failed. Now, they have been given the information they need to go back in time if they want to. In fact, they could choose to go really far back in time and really alter the shape of the campaign (like saving a powerful dwarven nation that disappeared). So far though, they have shown little inclination to actually go back in time and are instead simply trying to keep the BBEG from doing so. The upshot is that I am certainly not going to force the PCs to go back in time, but their decision not to will absolutely shape the world. The plot line represented by the time travel will continue to go on, it just has a different shape and ending than if they go back in time.
I think this is what Chris is doing. He's giving them an opportunity to get back on the previous plot thread, but he's not forcing it upon them. Either way though, it sounds as though that story line will continue to progress and the result will simply be different based on the decisions of the PCs. It sounds to me as though questioning the NPC, and keeping her alive, will make it easier to rescue the Emperor. Killing her or letting her die, will make it much more difficult - -maybe even resulting in the Emperor's death. The thing is though, when the original NPC was killed, it all but completely closed that particular plot line. There was no way to get the organization in question back into the story without another NPC. Had he really wanted to railroad them, the next NPC they met would have been part of the group too. Or maybe, all the notes about the group would have been on the body of the NPC, etc. Instead though, he took the cue and moved on, biding his time until it was appropriate to introduce another NPC that could again help move that plot line forward if the PCs choose to do so.
Of course, we'll never know for sure unless we join his group.
