I feel very strongly, that this event, is the end of the world. Not just a dream sequence, or a parallel world, or a dimension created by Judy to lock Laura, but our world. It was such an important event, that it changed everything about the Twin Peaks universe. The glitch scenes throughout the season was the result of what happened in the end. Things I have gathered:

# Since the nuclear test, and the advancement of the technology, the entities had a greater chance to enter our world. Each moment it opens new possibilities for them to alter the earth.

# The white lodge, as we saw a glimpse in the original run with Major Briggs, was depicted as heaven.

# The Giant was able to travel through realms, and aid characters, but now the building he is in, appears to be a vast prison in a dimension that seems to be an infinite sea without limits.

# If he was emanated from the white lodge, it either means 1: It is invaded or erased by the black lodge, or 2:  The Giant was one of the many entities that represent it, and only he and  the other lady we saw was locked in the prison. And, even from the first season, he seemed neutral to me. Unlike the angels.

# The influence of the black lodge has gone too far that it eroded the population, morals, and the overall quality of life. The Giant/Fireman?, Dido, and if there are other entities are either again have their powers diminished too much, they have limited information about certain things, and/or or they don't really care about our world at all,  have different agendas beyond comprehension.

# The entity that broke the glass box in New York, is now in our world. Maybe it takes form as complete decay, instead of a physical form after it's escape. Believe it's not Judy.

# Evryone including the Giant, seemed to be focused on Bob. Judy, as Hawk says, seems to be something that shouldn't be talked about, shouldn't be found, or searched for. The ones that searched it, lost in the realms of time and perished. If someone like Major Briggs gets destroyed, it changes many things. Thus making the idea of having the perfect courage of the soul, through black lodge to enter the white lodge, becomes obsolete in a way. There are other factors now. Other factors that mortals no matter how knowledge, courage, and love they have, have no information about, and shouldn't be dealing with.

# Very strange that, even Bob, which seems to much of a threat for everyone, doesn't know about Judy. He knows about the symbol of Judy, but strangely doesn't know what it is.

This leading to: He is unaware of his origin, and clueless. 1: His only intention is not getting back into the black lodge again, and that only. He no longer have fun. But a grim, bleak, serious entity is here.

# If Dale had known that Sarah was inhabited by Judy, he would've never taken Laura home. Possible reasons: 1: The Fireman didn't give enough information, and have another agenda humans can never understand. Further supporting his neutral allegience. Or 2: The Fireman, in his current condition, doesn't have any information about Judy.

#  The black lodge influence was at it's peak on earth. And Judy has been growing since 25 years inside Sarah, with all the energy in that house.

# When Cooper sees Naido, which I believe is not Diane at all, but another entity which had a greater role in all this, it triggers a massive change in the world. Cooper's image remaining there and his realisation is not because he is/was literally living in a dream. The living inside a dream I believe refers to how little they knew, how ignorant they are, by meddling with things they should'nt have. Even then and all he has left with is his hope. His "now" indescructible courage, and the trust upon the entity that guided him. 

# The planets align again, everything comes together. But this time everything is different. Reality warps and shifts on insane levels. Cooper takes Laura. And as they arrive, it happens. Cooper still doesn't give up.. he isn't lost. He just, tries to understand. This isn't how it was supposed to be. The guidance was wrong. He asks a simple question. Panicked yes, but... doesn't matter anymore. That was the moment everything ended. This wasn't a dream, it wasn't an alternate reality. It was all real. That was Laura, and it was our world. About the whisper, I think it was just the final moment in his memory before nonexistent.

# As the universe collapses, it's effects increase the space/time consistencies and glitches, and creates a ripple effect throughout the time, slowly erasing everything. Like how you can see a dead star even when it was dead probably hundreds of years ago.