When I go to the Museum of Nature, I start on the top floor and work my way down through the galleries, which are all off this central atrium. On the top floor, the special exhibit gallery is on the far side; the most recent exhibit had closed a few days before my visit. The Bird Gallery, usually on this level, is at present being moved down to the third floor, so I'll visit that the next time I'm in.
Stepping out from here into the Queens' Lantern gives views of the atrium from the other side. When the museum was originally built, there was a stone tower here; a few years later most of the tower had to be removed, as there were unforeseen problems with the soil beneath the tower. With the last renovation, the glass tower mimics the original, but is lighter. It presently features a large jellyfish hanging from the top, and features good views up Metcalfe Street, which leads right up to Parliament Hill.