I kind of think it’s more about doppelgängers — Mr. C has sort of trapped BOB in what I can best describe as a supernatural gallstone, and is harnessing the spirit’s power for his own benefit.
But BOB also works for MIKE/The Arm, and for the past 25 years they’ve been starved for garmonbozia. So I view their motivations as primarily trying to get BOB back, and helping good Coop is a way to do that.
The Fireman has a bit of a divergent agenda, as he seems to want to destroy BOB, which Freddy’s magic glove appears to do. So with that in mind, maybe MIKE didn’t help Coop to go back in time to save Laura Palmer, but rather he engineered a scenario where BOB was never trapped in Mr. C and subsequently never destroyed.
Although, the dead man in Carrie's home looks like BOB, so I suspect BOB
was destroyed. However, there's clearly something bigger going on: my suspicion is the Judy has got into the world the Fireman comes from and, in effect, the Black Lodge has invaded the White Lodge, destroying any balance between the two.
I'm a 'season four' person. I know many people say the ending of season three was 'perfect', but many people said the same about the endings of season two and FWWM. To me, BOB was - in computer game terms - a 'level boss'. BOB's gone, but now we're on the 'next level': a different reality version of Twin Peaks and the opponent is, perhaps, Judy herself. Cooper was supposed to become 'Richard', but hasn't done so... at least, not yet. Carrie appears to have had Laura Palmer's memories buried for many years. Laura escaped death, meaning the history of the original series changed, but now she and Coop have a new battle to fight. So Coop/Richard and Laura/Carrie need to find this reality's Gordon Cole and fight the next, perhaps final, battle.
As for the Lodges and their inhabitants, we don't know how they manifest in this new reality. Could they be manifested as real people and places, rather than spectral supernatural beings? Will they help or hinder him?
Presumably Red will become a significant foe, given he was set up in the previous series. Will Shelly be with him or is she 'someone else' who looks like Shelly? Does a character played by Heather Graham run the RR? Who will help Coop in a reality where the One-Armed Man and the Little Man no longer exist in their past forms?
And, on a simple level, the One-Armed Man was always broadly on Coop's side. The Arm evolved and one version appears to be 'good' now. Consequently an overtly 'bad' version of it appeared too.
And there remains the question of where Coop has been all this time. His meeting with the Giant - now called the 'Fireman' - appears to be like James Bond meeting M. His meeting with the One-Armed Man and the Arm gives the impression he's been away for a long time, as the Arm's 'evolution' has to be explained to him. Coop is wearing different clothes and has a different hairstyle. He appears to have become some sort of agent for the Fireman. He takes the 'Richard and Linda' mission orders in his stride, as if receiving these sorts of orders is pretty normal.
