After the clash between Kuzan and Sakazuki during the two-year timeskip, Sengoku realizes that the Navy have become far too corrupt, and forms SWORD, a secret unit dedicated to battling the evils the Navy will not take care of.

Shizuka Joestar and a new ally goes on an adventure across New York to finish what her father started: Defeating the last remnant of the Pillar Mens terror.

The character's who everyone was dying to see developed, the bounty hunters of East Blue, Johnny and Yosaku, go on their own adventures as they attempt to find a place in an Age of Pirates they are comically to weak to survive in.