Though it's somewhat divisive among fans, Fire Walk With Me is nonetheless an important chapter in the Twin Peaks story. During last week's revival double feature, creators David Lynch and Mark Frost dropped a major reference to the prequel movie. Phillip Jeffries, who was played by the late, great David Bowie, was apparently still around and in communication with BOB/Cooper in 2014 when the revival takes place. Like many of the characters in Twin Peaks, Jeffries is steeped in mystery. It certainly doesn't help that he had only a small role in Fire Walk With Me, so there’s little to go on. However, Jeffries was an important character who (according to Harry Goaz, who plays Deputy Andy Brennan) was supposed to appear in the revival - and there's a faint possibility that he still might.
Bowie away passed in January 2016, right in the middle of the eight-month filming of the revival series. Though he was quite ill at the time and working to finish his final album, Blackstar, it is possible that he filmed something new for the series. Twin Peaks was notorious for its secrets - even keeping some from its own cast. At the end of season 1, it looked like Catherine Martell (Piper Laurie) was killed in the Packard Sawmill fire. She returned in season 2 as Mr. Tojamura - a Japanese businessman - and nobody in the cast knew it was her underneath the makeup until it was time to film the reveal. The revival has also been filmed around an actor's sickness already; Catherine Coulson, the beloved Log Lady, filmed her scenes well ahead of the production schedule due to her terminal cancer diagnosis. To keep spoilers from leaking out, Lynch only gave his actors fragments of the script - specifically only the scenes they themselves were in. Only Kyle MacLachlan and Sheryl Lee read the full script. With that in mind, it's possible that Bowie filmed his relevant scenes as part of a closed set, in order to preserve the surprise.
Bowie's character in Fire Walk With Me was an FBI agent who was a peer of Gordon Cole (Lynch). They graduated from the academy together and were longtime friends before his disappearance in 1987. In Fire Walk With Me - which takes place in 1989 -Jeffries walked off the elevator as if nothing happened, and confronted Cole in the Bureau’s Philadelphia office. He babbled incoherently about a woman named Judy before disappearing through a portal and ending up in Buenos Aires.
From what we understand, Jeffries’ story goes as follows: he was in Washington state - the same state that Twin Peaks exists in (besides the state of confusion) - and was investigating the apartment of a woman named Judy. Fun fact: Judy, going by the behind the scenes data, was at one point possibly going to be revealed as Josie Packard’s (Joan Chen) sister. Judy lived above a bodega; the apartment had access to or itself was an extension of the Black Lodge. Shown in the film as a standard apartment with the red drapes of the lodge phasing in and out, we see several of the ethereal entities hanging around there: the Man from Another Place and BOB; Jumping Man, The Electrician, Mrs. Tremond, Mrs. Tremond's grandson and the Woodsmen.
It’s likely that Jeffries was held captive in the Black Lodge the way Annie Blackburn (Heather Graham) was - that is, he may not have a doppelganger running around. By the time of the revival, which is set in 2014, the evil entity BOB has been running around in the real world as Cooper’s doppelganger. When captured, BOB/Cooper attempts to keep up appearances to Gordon Cole by claiming he has been working deep cover with Phillip Jeffries. He does this because he knows it will play to Cole’s sympathy and curiosity. However, the relationship to BOB and Jeffries is more complicated.
In the second episode of the revival, BOB/Cooper murders his hired goons, Ray and Darya, because he learned that Phillip Jeffries had hired them to betray and murder him. After dispatching them, BOB/Cooper contacts someone who claims to be Phillip Jeffries, and Jeffries gloats that he knows the doppelganger is going back to the Lodge.
Of course, the voice on the line is substantially different from Jeffries’ southern twang, which leads us and BOB/Cooper to wonder if this is the real man. There is also the question of Jeffries’ intentions. He seems to be adversarial to BOB/Cooper, but the attempted hit may have just been an opportunistic thing. From what we’ve gleaned over the first four episodes, BOB/Cooper has developed a large criminal network across the United States and into South America. It’s possible that, given his own time in the Black Lodge, Jeffries was able to identify that the doppelganger was a doppelganger. He even knew that Cooper would eventually be replaced by BOB, given his terrified reaction to Cooper in Fire Walk With Me, taking place months before Coop's fall.
Jeffries’ name-dropping of Garland Briggs (Don S. Davis) is also important. It’s alluded to in both Mark Frost’s The Secret History of Twin Peaks and in episode 4 of the revival that the major was killed in a fire; it is strongly suggested that BOB/Cooper was involved in the death. As the only person to ever escape the Black Lodge—Annie Blackburn did too but she remained in a catatonic state—it’s quite possible that over the course of the last 25 years, Jeffries has been trying to send BOB/Cooper back. Maybe he’s studied the lore of the woods around Twin Peaks and the Blue Rose cases that the FBI has in their database. Jeffries could be the key to understanding the Black Lodge, getting the real Cooper his memory back and stopping BOB once and for all.
Or, it could be that Jeffries has turned evil.
It’s worth reiterating that when pressed, BOB/Cooper revealed to the FBI that was working with Jeffries. He could, of course, be lying for the reasons above, but we also learn it’s an excuse he’s used before. A few years after Cooper’s disappearance (no one knew he was a doppelganger), he contacted FBI agent Albert Rosenfield (Miguel Ferrer). Albert was close to both Cooper and Jeffries and when Cooper said he was working alongside the man, Albert did his best to help with Coop’s problem. This led to Albert giving Cooper the name of their man in Colombia, who was executed shortly thereafter.
Perhaps Phillip Jeffries was eventually given a doppelganger, or was so corrupted by the evil he was exposed to in the Black Lodge. Given the “evolution” of The Man From Another Place in the original series to the electric tree/brain-stem thing we saw in the revival, it is possible that Jeffries return in another form, even if Bowie himself doesn't reprise his role. Whether this Phillip Jeffries is the real one—and if he is on the real Cooper’s side or not—is totally up in the air. After all, this is Twin Peaks.