This essay was written by me.
Warning: Unless you've seen all 26 episodes of Noir, you're in for major spoilers!
Noir is just one of many anime with a controversial ending but, at least in my opinion, it's not quite as hard to explain as others. But still, it could be hard to interpret exactly what the ending means, so I'm going to try and explain my opinion of it as best as I can.
The way I saw it, the series ends with Mireille and Kirika leaving the Manor after fulfilling their goal of going on a "pilgrimage" into their pasts. The main conflict throughout the series is that they were trying to figure out who had been secretly manipulating their lives and for what reason. In the end they had finally gotten their answer; the Soldates, particularly Altena, for the purpose of making them the next Noir ("nurturing the saplings," as Altena puts it.) So what do they intend to do after finding their answer? Well, I think the reason the last sounds we hear at the end of the final episode are gunshots is simply to imply that Mireille and Kirika have once again taken up their guns and gone back to their old way of life (being assassins; one shot is sounded for each of them.) But this time they are no longer tied down by the darkness of their pasts, which I think is signified by the final scene; the watch lying broken and by itself in the deserted Manor. They'll continue being assassins and "bearing the sins of mankind" but not because they are Noir, but because it is the path they have chosen for themselves. But because of their adventure together and the stronger bond that formed between them as a result, they're satisfied with this. And instead of being lost alone in the darkness like they were before, now they're going to "search for the light" together, as Mireille tells the Soldates in the end.
Well, I thought Noir had a good ending, and sort of uplifting too considering how "cold"(but truthful) most of the series was. Unfortunately, for such a beautiful and thought-provoking series, I think Noir is one of the more underrated anime. But hopefully after reading my explanation for the ending, you have a better appreciation for it ^_^