Anathem's ending?

I finished reading Anathem last night.

For the first 400 pages I thought this was the most intellectually interesting and stimulating book that Neal Stephenson has written to date, although I wonder whether someone not in the physical or mathematical sciences would find it so interesting. As a venue for a discussion on metaphysics its brilliantly written.

The ending? I'm a little confused by the last 100 pages, in particular the last 20 or so pages. Stephenson's endings to his book have always been the weakest part of his writing, so in perspective this is better than most of his endings. Maybe I'll have to read it again...