One of the common misconceptions is that David Lynch is giving us an epic struggle between good and evil in Twin Peaks. This is a deliberate misdirection on his part. In looking at his entire body of work, I think it’s clear that good and evil do not exist in Lynch’s world.
The biggest clue lies in the most iconic setting of the series. Some people call it the Black Lodge. Others call it the Red Room. But its red curtains and black and white zig-zag floor pattern (Lynch’s take on the floor of the masonic temple, also used by many magical orders such as the Golden Dawn), don’t really give us a strong impression either way. I think the most accurate name for this place is simply The Lodge. Because the White Lodge and the Black Lodge only exist as social constructs among its members. The members themselves continuously try to influence the nature of reality and form factions that they may at times call White and Black, but they are all members of the Lodge. (The word lodge itself is used to refer to Native American gathering places and masonic groups).
There is no Good Cooper and Bad Cooper. There is just an entity that has been extremely out of balance that has been divided by his own wants and needs. The goal is not to destroy one or the other, but to unite them.
Does that make sense?
If anyone wants to hear more on Western occult symbolism in Twin Peaks let me know. Folks would arm themselves well by taking a closer look at the Secret History of Twin Peaks, and two of the very real historical figures mentioned—Jack Parsons and Aleister Crowley. You also wouldn’t go wrong by studying the works of the UFOoligist Jacques Vallée.