Twin Peaks: The Return was clearly intended to be open to interpretation. Nevertheless, I wanted to see if I could come up with a cohesive explanation of the events. I have combined some of my own interpretation with a few other ideas I have seen floating around in various posts. I don’t see this explanation as definitive in any way and other people will inevitably reach different conclusions… which is ALL part of the fun : - )

There was a lot of detail to cover, so I have divided it into sections to make it easier to get through. Please let me know your thoughts.

The plan (killing two birds with one stone):

After Cooper becomes fully awakened, he is clearly working through a very specific plan, which apparently also involves Major Briggs, The Fireman and Phillip Jeffries. The goal of this plan (one stone) seems to have been to defeat BOB and Judy (two birds). A lot of people have interpreted the scene in episode 17, where Laura disappears near the White Lodge portal (after Cooper goes back time to save her), as the plan going wrong. I don’t think this is the case though. In the earlier scene where Andy is with the Fireman (episode 14), one of the images we are shown is the electricity pole placed outside Laura/Carrie’s house in the alternative universe. This means that the Fireman already knew about the alternative reality and it is likely that several other characters (including Cooper) did too. There is also Cooper’s earlier scene with the Fireman (episode 1), where the Fireman runs through the plan with Cooper, who then states that he understands. It isn’t entirely clear when this scene is supposed to have taken place, relative to the rest of the series, but it still suggests prior knowledge of the alternative reality.

If we also assume that Jeffries knew about the alternative reality (and the plan), then Cooper’s scene with him (episode 17) begins to make more sense. When Jeffries shows Cooper where to find Judy, we are shown a figure eight with a dot on it, which then flips over and the dot moves round so that it is in the same location again. The simplest interpretation I can think of for this is: different side, same place. ‘Different side’ meaning over in the alternative reality. ‘Same place’ meaning where Judy is currently residing in the main reality i.e. the Palmer house. Jeffries was giving Cooper instructions on where to find Judy, but after he had gone back in time to save Laura. It seems they knew Judy would cross over into the alternative reality, after sending Laura there. But with Laura still alive, this provided an opportunity for her to play her part in the plan to defeat/contain Judy. In terms of Judy residing in the Palmer house, there is more on this below, but importantly Garland Briggs and the Fireman were shown watching the Palmer house (in episode 17).

The events which take place in the alternative reality:

There have been very different interpretations of the final scene, so it is not possible to say whether the plan outlined above was ultimately successful. However, despite the dark nature of the scene, I think there is scope for some (cautious) optimism. I believe Laura/Carrie screaming in the final scene represented a form of awakening for Laura and a realisation of who she is and of her previous existence in the main reality. We know that Laura was created by The Fireman as a force for good, so her awakening would be an important and necessary step she needs to take; something which is analogous to Cooper waking up and remembering who he is earlier in the series. The lights going out in the house and the flash of electricity could be interpreted as confirmation of the evil that resides within and a removal of the facade of normalcy we are initially presented with when Cooper/Richard knocks on the door (although the use of the names Tremond and Chalfont were already indicators to the audience of something sinister). Cooper asking, ‘what year is it?’ may have shown that he was unsure whether they had arrived at a time when Judy was actually residing in the Palmer household. However, the lights going out suggest that Judy was there after all.

As to the nature of the alternative universe, we are only given a limited amount of information about this, which is fuelling a lot of speculation. However, we do know that characters from the main reality appear to exist in the alternative reality, but with different identities. When Laura ends up in the alternative reality, most people believe she becomes Carrie Page. However, a better interpretation could be that her consciousness was merged/embedded within Carrie Page and left dormant until Cooper took her back to Twin Peaks in the alternative reality. 

This would help to explain what happens to Cooper himself, after he crosses over to the alternative reality and his personality begins to change. His motives still seem good and he appears to have retained his memories as Dale Cooper, but he also seems colder and more detached. I think this could be interpreted as him becoming merged with Richard (who, as a character, we know very little about), but not becoming completely subsumed like Laura – and also (apparently) like Diane (following that uncomfortable sex scene). It is also possible that Richard shared some similarities with Cooper’s (now deceased) doppelganger from the main reality, given that both his personality and his car are quite ‘Dark Cooper-esque’. 

At any rate, Diane appeared to be aware of the change taking place within Cooper/Richard and also seemed to lose herself within Linda, perhaps becoming dormant like Laura. This process of ‘merging’ into the new reality might also explain why features such as the hotel and the car change after Diane/Linda leaves; reality around them is adjusting itself to merge them into the lives of their alternate selves. Diane seeing her doppelganger is less explainable. It is also not clear what Diane’s role in the plan was at this stage.

The final events taking place in the main reality:

Dark Cooper finally arrived in Twin Peaks, but what exactly was his end goal? On this point, it’s easy to overlook the fact he was possessed by BOB the whole time. I believe the end goal was to reunite with the Experiment… and that this was BOB’s goal, as opposed to Dark Cooper’s. Conversely, Dark Cooper’s main goal seemed to be about avoiding going back into the Black Lodge (as well as killing Good Cooper, who he perceived as a threat to his existence). When Dark Cooper believed he was talking to Jeffries on the phone in episode 2, a plausible explanation is that he was actually talking to the Experiment, who wished to be reunited with BOB but who was apparently unconcerned about Dark Cooper. Had BOB been successful in his end goal, I believe he (and Dark Cooper) would have reached the Palmer house. However, he was stopped, as the second set of coordinates (like the first set) were a trap. Instead, BOB and Dark Cooper were intercepted and sent to the Sherriff’s station. This explains the White Lodge scene where Major Briggs and The Fireman are shown watching the Palmer house, but switch this location for the Sherriff’s station instead. As a result, BOB was destroyed by Freddie and Dark Cooper was subsequently sent back to the Black Lodge by Good Cooper. 

The Experiment/Mother remained a threat however and the force for good created by the White Lodge (Laura) remained dead, which is where the time travelling and alternative reality aspect of the plan needed to come into play. They needed Laura alive and un-murdered for their plan to work. This plan will presumably have a positive effect on the main reality, although we don’t get to see much of what happens after the main reality timeline is altered by Cooper. Pete gets to go fishing and Janey-E and Sonny Jim get their new Dougie, but we can only guess at the rest. For example, what would be the impact of Laura disappearing? Would she have ‘gone missing’ rather than being murdered, or would she have never existed at all? There would certainly be some time paradoxes thrown up in terms of the plan, although I’ll avoid getting into any of that…

How Judy fits into all of this:

As others have suggested, the ancient evil called Judy (or Jao Dei) is almost certainly the ‘Experiment’ that we see in episodes 1 and 8, which appears in the glass box in New York and which gives birth to BOB in the Trinity explosion. Judy is also almost certainly the ‘Mother’ the American Girl refers to in episode 3. This makes sense, given the Experiment is the ‘mother’ of BOB. Also, the Experiment arrives in the box in New York shortly after Cooper. Given that Cooper then arrives in the ‘purple zone’, it makes sense that the entity which arrives shortly afterwards and begins banging on the outside, is the same entity which we saw in New York. This must also be the same entity we see on Dark Cooper’s playing card (the entity BOB is looking for) and on Hawk’s map ‘under the moon on Blue Pine Mountain’ (as later stated by the Log Lady in episode 15). Note that Blue Pine Mountain is where the White Lodge portal is located, as well as being a place where Experiment/Mother/Judy has some influence. 

Could Blue Pine Mountain be another soft spot between the two realities (a bit like the location at 430 miles), but one that Judy has a hold over? Maybe placing soil in your pockets provides a way of staying grounded in the main reality, when passing through this location. When Laura disappears to the alternative reality (and Cooper subsequently disappears to the Black Lodge), neither she nor Cooper were carrying any soil. They were also walking on a moonlit night (i.e. under the moon on blue pine mountain). 

There have been a number of theories concerning Sarah Palmer and her potential links to Judy/Experiment/Mother, as well as her possibly being the girl possessed by the bug creature in 1956. I do not subscribe to the theory of her being the girl in 1956. Geographically this does not fit with what we know about Sarah Palmer and the girl looks older than 11 (which Sarah Palmer would have been at the time). There has also been speculation that Sarah Palmer has been possessed by Judy/Experiment/Mother from the beginning (via the bug creature), which also does not make sense. If BOB and Judy/Experiment/Mother had both lived in the Palmer house at the same time, then BOB would have known where to find her as soon as he left the Black Lodge at the end of Season 2.

However, there is a strong evidence that Sarah Palmer is under the influence of Judy/Experiment/Mother by the beginning of Season 3. The reveal of the void behind her face and attack on the truck driver (episode 14) is the most obvious pointer. There are clear visual (and sound) similarities between this and the void we see in the glass box in NewYork, even if we don’t directly see the entity itself in the Sarah Palmer scene. The nature of the attack is also similar to what we see in New York. Sarah Palmer’s unusual behaviour throughout the season suggested something was wrong before this though (e.g. the grocery store where she specifically states that something happened to her). Her voice also sounds low and unusual during several scenes, so it’s plausible that Sarah Palmer spoke to Dark Cooper during the aforementioned phone call in episode 2, acting as a vessel for Judy/Experiment/Mother. Additionally, the bowl of garmonbozia we see in her living room (episode 13) suggests something sinister is going on

Furthermore, all roads seem to point to the Palmer house. As I mentioned before, this seems to be where Dark Cooper and Bob would have ended up if they weren’t intercepted by Garland Briggs and The Fireman. It’s also where Cooper and Laura end up in the final episode, after travelling to the alternative reality. Sarah Palmer (in the present day main universe) was obviously angry when Cooper changed the timeline in the main reality, by saving Laura (and the sounds we hear in this scene certainly don’t seem ‘human’). Laura suddenly being alive would pose a threat, so an obvious explanation is that Judy/Experiment/Mother was somehow able to send her into the alternative reality, where she became embedded within her alternate self. The scratching sound we hear before Laura disappears (the same scratching sound we hear in Cooper’s scene with the Fireman in episode 1) is also likely to be Judy/Experiment/Mother (what the Fireman says in this scene certainly seems to support this idea). Also, we hear Sarah Palmer’s voice calling ‘Laura’ in the final scene of episode 18, just before Laura screams, again linking Sarah Palmer to Judy/Experiment/Mother. Much of what we see in the alternative reality backs up the idea that it was Judy/Experiment/Mother who sent Laura there. We see the familiar electricity pole outside Laura/Carrie’s house, the model of a white horse on her mantelpiece, and the names Tremond/Chalfont crop up, all indicating dark influences. Most obviously though, Laura is working at a diner called Judy’s.

Some additional thoughts: 

There is a potential flaw in the above, in that Dark Cooper doesn’t know who Judy is when he meets with Jeffries. If Judy is BOB’s mother, then surely Dark Cooper should be aware of Judy too right? Well… perhaps not. BOB possessing Dark Cooper does not necessarily mean that Dark Cooper will know everything BOB knows. For example, Leland spent a long time totally oblivious to the fact the be was sexually abusing his own daughter while under the influence of BOB. Dark Cooper may well be in the dark about BOB’s goals.

Who is the girl in 1956? In truth, it’s not possible to say for sure - and I am yet to see an obvious link with any of the characters on the show. However, both Audrey and the Evolution of the Arm refer to ‘the little girl who lives down the lane,’ repeating the same words exactly. To my knowledge, the girl in 1956 is the only character which fits with this description in a literal sense. Is this therefore ‘her story’? In other words, could she be ‘the dreamer’? The last shot of her shows her in a state of REM sleep after the creature crawls into her mouth. Perhaps she could be possessed and acting as another vessel for the dark forces unleashed in the Trinity explosion, with her dreams/thoughts perhaps manifesting in reality and influencing events. The series has dealt with tulpas/thoughtforms, so this would be an extension of that idea. I’m not saying this idea is correct, but it’s just a thought I had…