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Zeboim Ruins is ruined remains of the ancient megalopolis city-nation known as Zeboim that used to exist in the Aquvy region 4000 years ago. After suffering a large-scale nuclear disaster, the entire nation was sunk beneath the sea and forgotten. Some portions of Zeboim sunk into air pocket caves and were accessible from the surface. One of these places was the laboratory of nanoscientist Kim Kasim, and a section of the city accessible by using an elevator hidden away in a lighthouse. The city section underneath the Lighthouse is only accessible at the end of the game. Down there a side quest can be completed that reveals details of the last days of the Zeboim civilization, concludes Big Joe's wacky "storyline" and his expensive Gear shop and transforms Emeralda Kasim from a little girl into a young woman which increases her stats.
Zeboim is likely a Biblical reference to a destroyed city.