This place is said to have been abandoned for a very long time. It was made for 700 people but only 250 skeletons were found. They say that it could have been a quarantine site.
In the game....Edit
Macchu Picchu is one of the places with a Malice Seal that Lady must open in order to summon the Gate. There are lots of puzzles including opening doors with coordinating colors to your "Mask" key item. Killer will attack the party so that Lady can go furthur.