In the Victorian era, the British Empire is bustling with the energy of the steam-powered industrial revolution. Following in the footsteps of his famous family of inventors, James Ray Steam enjoys his youth in Manchester helping at local factories and stealing components for his own creations. One day, he receives a package containing a strange ball with an attached valve from his grandfather, who has been working in the United States alongside Ray's father. However, it is not long before people from the O'Hara Foundation storm into his house demanding he hand it over. Confused and afraid, Ray attempts to flee to the home of his grandfather's colleague, Robert Stephenson, with pursuers hot on his trail. While Ray seeks to piece together the secret of the ball and discover the power it contains, it seems practically everyone in the British Empire is ready to seize it from him.

Shinya Kougami continues to wander the Southeast Asian Union (SEAUn) away from the eyes of the Sibyl System in Japan. While traveling through the Tibet-Himalayan Alliance Kingdom, Kougami encounters Guillermo Garcia—commander of a paramilitary group attempting to unite the local factions and bring peace to the war-torn nation. Wary of joining another mercenary group, Kougami declines to join his cause, but agrees to be driven to the nearby Tibetan capital by one of Garcia's men. However, Kougami's plan to remain uninvolved is short-lived when a bus of refugees are ambushed by armed guerrillas. Among them is a half-Japanese, half-Tibetan girl named Tenzing Wangchuck. Impressed with Kougami's fighting prowess as he single-handedly takes the attackers out, Wangchuck requests him to teach her how to fight so she can take revenge against the warlord who murdered her family. Knowing first-hand that there is no turning back to the person you were once you take a human life, Kougami is initially reluctant to accept her request. But faced with the girl's desire for vengeance that mirrors the haunting abyss inside his own heart, will he train her?

On a sunny afternoon in her Paris apartment, assassin-for-hire Mireille Bouquet receives a strange email from Kirika Yuumura, a young student from Japan, inviting her to make a pilgrimage to the past together. Initially thinking the email is nonsense, she changes her mind when it begins playing a song that she recognizes from her youth. Upon first meeting each other in person, the two are suddenly ambushed by gun-wielding men. While Mireille is capable of fending off the assault, she discovers that Kirika is quite adept in combat situations after she takes out several gunmen on her own. Despite her proficiency at killing, Kirika laments her inability to feel remorse for her victims. In addition, Kirika apparently has no memory of how she came to acquire the skills she possesses or even of her real identity. Sensing shared history between them, Mireille agrees to team up with Kirika, and together, they embark on a journey to uncover the mysteries of their pasts. Operating under the codename Noir, the duo's fragile alliance is tested as they begin accepting jobs, each one bringing them closer to the truth of who they really are.

With reports of monsters terrorizing the reactor at Mount Nibel, the Shinra Electric Power Company dispatches their elite fighting force SOLDIER to investigate. Accompanied by fellow SOLDIER First Class Zack Fair and a small contingent of company guards, the war hero Sephiroth is to assess the condition of the Mako reactor at the behest of the company. In Nibelheim, the village that the reactor powers, Sephiroth discovers the source of the monsters and the origins of Shinra's legendary Jenova Project. Running through the woods months later, Zack is no longer the hero he once dreamt of becoming. He flees from the General Affairs Department of the Shinra Electric Power Company, better known as the Turks, who desperately seek to bury the evidence living within the two.