Confusion over Atlantis history

Hi,

Did anyone else get confused by all the Atlantis history? We know Nemo destroyed his country 13 years ago by sabotaging the Tower of Babel, and near the end it is clearly stated his country (and the birth place of Nadia) is the Blue Noah in Africa. However, in the episode where the Nautilus goes to Atlantis (presumably the 3rd Noah spaceship sunken 12,000 years ago), it is implied that this is the place where Nemo did his deeds, i.e. the mass grave, Electra's account of the place destroyed by Tower of Babel, etc. Very confusing, or did I miss something?

Thanks