One critical point that has been made very clear from the beginning is that the returning Twin Peaks is not a remake. Nor, interestingly, is it set immediately after the events of the original show. It is a sequel that is set in the present, 25 years after Laura Palmer's prophetic declaration about seeing Agent Cooper again in the future. There will be allusions to the original series' storylines but plenty of new material too, with Frost insisting that:
I think there will be a lot of things that people have wanted to know over the years that if they pay close attention, they are going to be satisfied... I think you can safely say that the mystery in Twin Peaks as we started to explore more is very large, there are many aspects to it and the hope is that people will find things that they are interested in in all sorts of things related to the larger mystery. And that will include all the storylines we've dealt with up until now... There will be a very strong central storyline.
Whether or not Laura's death will still be a central theme is unconfirmed, as is the question of whether another mystery will drive the narrative, but it is safe to assume that the mythologies of the Black and White Lodges will be studied. Again, Frost notes, "the seeds of where we go were planted where we've been." It is also worth noting that Frost regards the show's prequel film, Fire Walk With Me, as canonical. Given its insights into the Lodges, many of its themes will probably feature heavily in Season 3.