Complex sentence: The first chamber was meant for worshippers to congregate in a large rectangular hall, and the second, a small, circular, domed chamber for worship, this inner chamber probably had a small stupa like structure, at some point, though they are now empty.
Split into simpler sentences: The first chamber was meant for worshippers to congregate in a large rectangular hall, and the second, a small, circular, domed chamber for worship. This inner chamber probably had a small stupa-like structure, at some point, though they are now empty.