FBI Agent Dale Cooper found a way into the other-dimensional Black Lodge in pursuit of his mentor Windom Earle. But Cooper was trapped in the Black Lodge and replaced back on Earth Prime-Time by an evil doppelganger - some evil spirit who only assumed the human form of Agent Cooper. (Based on the reflection in Cooper's cracked mirror, it most likely was either BOB or in communication with BOB.)
Knowing it could never maintain the illusion of the impersonation under constant scrutiny by those who knew Cooper, especially at the FBI, the doppelganger would probably have quit the Agency soon after.
That seems to be the likeliest scenario for the doppelganger's storyline. Anything extrapolated after that would be conjecture.
And as you've probably guessed, I've got one of those.....
The "Dark Dale" would probably need a power base from which it could carry out its evil designs, which perhaps included bringing others of its ilk over from the Black Lodge dimension.
Calling upon Dale Cooper's reputation as a former FBI agent, it could be that this "Anti-Dale"* set up its own security and protection corporation, a la the real life Black Water Corporation. As the world became more dangerous throughout the nineties, but especially after 2001, there would be quite a demand for such services. The doppelganger's agency could have built up quite a reputation, to the point where its clientele might feel comfortable in entrusting the agency with their financial and/or political information.
And the doppelganger would have collected this and analyzed it all in preparation for the time when the Black Lodge dimension wanted to take over Earth Prime-Time.
However, for alls I know, Anti-Dale was defeated before any of its plans could reach fruition - maybe by Mr. and Mrs. Mulder (C'mon! They must be married by now!); perhaps by the Winchester Brothers; or it could have been Buffy Summers and her Scooby Gang; even Carl Kolchak and his namesake nephew could have had a hand in its downfall. (I doubt it was by the firm of Spencer, Tracy, and Kong.)
No matter how it happened, I don't think the doppelganger is still existing as Dale Cooper, not that it means the real Agent Cooper has been returned to Toobworld. It's just that if Anti-Dale did have designs on Earth Prime-Time, wouldn't he have carried them out by now? Even a soap opera doesn't drag out a storyline that long!
But the security firm it established could still be in existence even after its death/departure from Toobworld. And we may have been given proof of its existence recently, which is why I came up with this theory.
In the second episode of 'Undercovers', Steven and Samantha Bloom were in pursuit of two brothers whom they believed were responsible for the kidnapping of a scientist skilled in the making of nuclear triggers. The brothers had gone rogue, separating themselves from the security firm for whom they worked: Black Lodge Protection. The doppelganger probably gave the firm that name in order for its other-dimensional brethren to easily locate him once they crossed over from the world of the Black Lodge.
It's an idea, and not likely to be either proven or dismissed... unless David Lynch and Mark Frost finally do get around to bringing the story of 'Twin Peaks' up to date. And they probably won't do that until 2016 - that's when Laura Palmer said that she would meet Dale Cooper again......
A big thanks to Andy for his help on the last part of this post!
* Which do you like better - Dark Dale or Anti-Dale? Or is there something even better out there? I'd love to use a term like "Walternate" from 'Fringe'......