At the climax of Chapter 1 you have to deal with Darth Jadus, offering a few different possibilities, one of which talking him down and having him take off to do whatever he intends to do before returning. I mention this in the event that it caused this bug:

After Jadus and subsequent convo with Watcher Two, you are told to leave the ship. I did just that and went to use the holoterminal. Instead of being told to return to DK and all of that, I was put immediately into Chapter 2 with Watcher Three telling me that they have to cut my time off short.

I didn't get to deal with the lunatic sith or speak to Keeper before he gets a promotion. Granted, it probably doesn't affect too much of story later on but it kind of takes away from the immersion.

Perhaps this was an unexpected result since they don't seem to have missions where you return to fleet and then go back to your ship for the next chapter.

At any rate, I've made a bug report but was curious if others have experienced the same thing or perhaps have a work around for any future playthroughs in the Agent Story.