Have you visited the Wolf's Den? There should be a "!", after that the game tells you to go to the Dark Swamp, after fighting an enemy the game tells you to go to Misty Abyss, you should see some "!" again.
Ah, well if you did all that, then all that's left to do is report to Bernard/Logan. That's it so far when it comes to (this) story content in this (0.40) update..
