NB: I wish I could claim credit for the following insight, but actually it was emailed to me.
As a matter of style, Moore's works have always tended toward disorganization; as one commentator put it, he wanders about like magpie, picking up anything shiny and sticking it into his nest, wherever it might fit. It's his style, and it works for him,
But Bowling is exceptional. A film which clearly begins with a theme of firearms, firearm owners, and firearm organizations being dangerous or even evil, ends with a conclusion that having lots of firearms and firearm owners is not a problem after all. We start with the Columbine killers and Michigan Militia and Terry Nichols, and end up talking in his utopia, taking to its resident gunnies about how easy it is to acquire guns.
We don't have a chronology of Bowling, but Moore's statements suggest he began work on Bowling in 2000. He did a lot of the filming over summer, 2001. The K-Mart demonstration occured in June 2001. Moore gave a speech discussing Bowling in July of that year. And the earliest versions of Bowling have a 2001 date assigned, and were showing in February 2002.
It's reasonable to assume that by winter 2001, Moore was done filming, well into post production, perhaps ready to put his movie in the can.
Then comes 9/11.
Moore's comment on that shocking event (since deleted from his website, but available elsewhere) makes it apparent that he was indeed in the process of editing Bowling, and was struck by an incongruity:
I cannot go to work. But I have a film to finish. Our editor has been unable to make it in from New Jersey, but he is there now waiting for some word on what to do.
I can't even think about this movie. I don't WANT to think about it because if I think about it I will have to face an ugly truth that has been gnawing through my head...
This started out as a documentary on gun violence in America, but the largest mass murder in our history was just committed -- without the use of a single gun! Not a single bullet fired! No bomb was set off, no missile was fired, no weapon (i.e., a device that was solely and specifically manufactured to kill humans) was used. A boxcutter! -- I can't stop thinking about this. A thousand gun control laws would not have prevented this massacre. What am I doing?
Might it be that the disjointed nature of Bowling, the complete reversal of its theme in the last twenty minutes, stems from this sudden insight? Bowling started out as one movie, but ended as another? Or at least partially ended as another -- Moore didn't want to have to rework it from the beginning, and so just re-edited the last twenty minutes or so?
As thus cut the film is rather incongruous. After all, a large part of the beginning is devoted to attacks on the NRA and on Charlton Heston ... who argue that gun ownership is not a cause of violent crime, and gun laws are no solution. In the end, Moore ... agrees. Yep, they're completely right. Canada is full of guns and has low crime rates, so something else must be the explanation.