What causes uneven floors and can they be fixed?
Although it is impossible to say for sure without seeing the floors in question, I suspect it is a simple case of poor construction practice. The basement floor is most likely over a concrete slab. The floor may not have been leveled with framing. You did not mention what type of flooring was there, but I suspect the tile or carpet was applied to an uneven base.  The upper story floor was most likely built long ago on the existing joists, with the same un-level results. In either case, the only way to level these floors would be to frame a new subfloor level, then install new flooring over a properly installed subfloor. There is no trick or shortcut to fixing situations like this. This can be an involved and expensive project, not a good DIY for amateurs. 

As far as the fireplace is concerned, if the room in question was originally designed as a livable space, it is not uncommon to see a small fireplace. Before the days of central heating systems, many older homes (100 yrs ago) had multiple fireplaces. The concern by today's standards is if the assignment of flues is correct. By that I mean, how many and what type of combustible devices share a flue. There are strict rules on what fuels can share flues and an what elevation in a house. This is important as fumes or CO can invade through a flue from one device to another. Again, this would have to be inspected for safety.