Dirge of Cerberus: Final Fantasy VII
Reeve Tuesti, who used to be the Head of Urban Development at Shinra (and the remote controller of Cait Sith), is now the leader of the World Regenesis Organization, which looks after the planet and stops people from hurting it any more. Yuffie Kisaragi is another member of the organization, and several other characters from the original game provide the World Regenesis Organization with more help.