The following is a chronological list of events that take place in the Final Fantasy: The Spirits Within universe.
- On an unknown alien planet, an aggressive race fights a war that destroys their planet. A large chunk of the planet flies off into space, carrying with it several million of its inhabitants and fauna of various sizes. The flight through space kills the living organisms on the chunk, but they are imbued with such malice and suffering that their spirits remain as ghosts.
- Dr. Sid is born in June, in Toronto.
- Dr. Sid detects a strange energy force during a gravitational field extraction experiment and begins conducting research into spiritual energy, resulting in the Bio Etherium and the Gaia Theory.
- Douglas Hein is born in San Francisco.
- Several meteorites crash to Earth during the Leonid Meteor shower, the largest of which lands in the Middle East, among the Caspian Mountains.
- The wild-life of the world begins dying in the areas surrounding the meteorites due to unknown causes.
- Gray Edwards is born in April, in Chicago.
- Ryan Whittaker is born in July, in New York City.
- Jane Proudfoot is born in January, in Houston.
- Dr. Sid and his colleagues discover evidence of "Phantoms" being responsible for the mass of unexplained deaths that are occurring around the world.
- The United Nations establishes the USMF as its Anti Phantom Division. Forces from each nation begin their assault on the Phantoms by using conventional weapons.
- Conventional weapons are deemed ineffective against the Phantoms.
- More than 60% of the world's military forces are exhausted.
- The Phantom Cleansing Mission of Tucson is launched.
- The first Spiritual Energy Weapon is developed by Dr. Sid.
- The Barrier System Theory is developed, leading to the creation of the Barrier City project.
- The first experimental barrier is completed around Houston.
- Douglas Hein enters the Houston Military Academy at 17 years of age.
- Douglas Hein meets his future wife, a social worker dedicated to finding a solution to the Phantom threat.
- Barrier City construction commences for 130 cities and 1200 military facilities around the world.
- The United States Military Force enacts a country-wide draft to supplement the military forces for Phantom Cleansing Missions.
- Gray Edwards enters the Houston Military Academy at 17 years of age.
- Jane Proudfoot enters the Houston Military Academy at 16 years of age.
- The world human population has decreased from 10 billion to 300 million as a result of Phantom attacks.
- The development of the Zeus Cannon begins.
- Neil Fleming enters the Houston Military Academy at 18 years of age.
- Dr. Sid completes the first successful analysis of the Phantom Spiritual Wave.
- During consecutive training missions, squadron leader Gray Edwards and medical assistant Aki Ross meet and start building a relationship.
- The San Francisco Barrier City's barrier fails. Douglas Hein's wife and daughter are killed as the city is overrun and destroyed.
- The fourth World-Wide Phantom Cleansing Mission occurs.
- Douglas Hein is promoted to the rank of General.
- The Deep Eyes squadron (Jane, Neil, Gray and Ryan) is formed to conduct search and rescue missions throughout the Barrier Cities and wastelands.
- Aki Ross moves to the New York Barrier City to complete her doctorate.
- Aki becomes infected by Phantom particles after an accident during an experiment.
- Aki cuts herself off from people, including Gray Edwards whom she was still pursuing a relationship with.
- Dr. Sid temporarily contains Aki's infection using a chest plate to keep it in check.
- Discovering that her wave pattern was ideal to add to the Wave Theory, Aki starts searching for the remaining spirit patterns to complete the desired wave-form.