Two years after the events in Final Fantasy VII, a disease known as "Seikon Shôkôgun" or "Geostigma" is spreading through the planet. It seems to attack the children, mainly. This disease is believed to be caused by the body fighting the remnants of the material that invaded it at the end of Final Fantasy VII. Cloud Strife, haunted by his past and still feeling guilty for don't being able to save Aerith, decides to live a solitary life, away from his friends while running a delivery service called "Strife's Delivery Service", whose headquarters are located in Tifa's Seventh Heaven Bar. Also, she helps Cloud by taking care and watching over the orphans that have been infected with Geostigma, as well as keeping an eye on Barret's six years old daughter, Marlene. One day Cloud receives a phone call from the Shinra former president, Rufus, who asks for Cloud's services as bodyguard to keep him safe from the Silver Haired Men, and especially from a mysterious young man that responds to the name of Kadaj. Kadaj, in the meantime, along with Yazoo and Loz, is in the quest for "Mother" and chases Cloud, convinced that he knows her whereabouts. Kadaj yearns for the "Reunion" to take place... what could this "Reunion" be? Who are these Silver Haired Men? Could they be related to Sephiroth?