It begins with Squall the main protagonist and Seifer an antagonist fighting outside the Balamb Garden military academy, injuring each other in the process, which left distinctive scars on both of them. Meanwhile, Galbadia invades the Dollet Dukedom, which forces Dollet to hire mercenaries from Balamb Gardens branch of “SeeD”. The mission to aid Dollet is used as a final exam for the cadets, which is looked over for the lead instructor Quistis.
Squall passes the mission and is placed with Seifer and Zell. Seifer disobeys orders and leaves his team, Selphie is now forced to accompany the team for the rest of the mission. They succeed in stopping the Galbadian and Squall, Zell, and Selphie graduate to SeeD status, while Seifer is disciplined for his actions. During the graduation party Squall meets Rinoa for the first time, which he finds out to be the complete opposite as him.
Squall is now assigned with Zell and Selphie to aid Rinoa’s resistance faction in Galbadian-occupied Timber, they find out that a sorceress named Edea is behind Galbadia’s attack. The group now gets orders from Balamb and Galbadia Gardens to assassinate the sorceress. They are now joined by Rinoa, Quistis and Irvine to aid in the mission. However they fail the mission and the party gets captured, during which Squall’s party now learns that Seifer has joined the sorceress as her second in command.
After their escape escape, Edea launches a missile attack on Trabia Garden. Worried that Balamb Garden would be next the party splits in two. Squalls group returns to Balamb to warn everyone of the attack but sees that NORG (SeeDs financiers) has begun an internal conflict with Balamb which the party must first stop.
Selphie's team goes to the missile launch to stop the attack but fails. Squall accidentally activates Balamb Garden’s “Mobile Fortress” form which in doing so adverts the missile attack, but unable to control it, the Garden crashes into the docks of Fisherman’s Horizon. While the Garden is being repaired the party enters the village. The group is attacked by the Galbadian Army which are in search of a girl named Elllone, which use to live in Balamb Garden. They find out that Ellone has escaped to Esthar, the technological superpower of the planet.
Squall meets up with Ellone and is then told that she has been giving him flashbacks from 17 years ago in effort to change the present. The past memories are of Laguna and his two friends, Kiros and Ward. Laguna changes from being a Galbadian soldier then a defender of a small country village to the leader of a resistance movement against the Sorceress Adel to the President of Esthar.
Squall is now developing at a high rate, which is giving him anxiety issues since he’s become the leader of SeeD, and not to mention his attraction to Rinoa. While investigating Tribia Squall and his party realize that they (including Seifer and Ellone) were all in the same orphanage long ago (except Rinoa) which was run by Edea. They all later developed amnesia from the use of Guardian forces. They also find out that Cid and Edea started the Garden and SeeD in order to defeat corrupt sorceresses. After this realisation the army or Balamb Garden and Galbadia, led by Squall and Seifer begin to fight above the orphanage. Balamb then defeats Galbadia, the player finds out that Edea is just a puppet controlled by a even more powerful sorceress from the future by the name of, Ultimecia, which wishes to compress time into one single moment and is the reason why she seeks Ellone. Edea loses the battle with SeeD which forces Ultimecia to transfer her powers to another vessel and turned out to be Rinoa. Edea lives, but Rinoa was put into a coma, Squall become obsessed with waking Rinoa from her coma and goes to Esther to talk with Ellone in an attempt to save Rinoa.
Rinoa is now being treated at Esthar space station and Ultimecia uses her to free the Sorceress Adel from her orbital prison. Ultimecia then orders Seifer to activate the Lunatic Pandora facility, sending a rain of monsters from the moon to the the planet along with Adel’s shuttle. Ultimecia abandons Rinoa to transfer her powers now to Adel and leaves Rinoa floating in space. Squall rescues her and they return to the planet. When landing delegates of Esthar isolate Rinoa in fear that she still has sorceress abilities, which makes Squall break her out.
President Laguna apologizes and announces Dr. Odine’s plan to let Ultimecia possess Rinoa, have Ellone send Rinoa (and Ultimecia as well) to the past and then retrieve Rinoa back to the present, making Ultimecia achieve Time Compression, allowing Squalls group to confront Ultimecia in her time. To do this, Squalls team breaks into Lunatic Pandora, defeats Seifer an Adel, and gets Rinoa to inherit Adel’s powers. Time Compression then gets initiated Squall and the group travel to Ultimecia’s time and defeat her.
The planet now returns back to normal with Ultimecia dead, but however Squall is almost lost in the flow of time as he witnesses the origin of the games story. While a dying Ultimecia travels back in time to transfer her powers over to Edea, Squall tells Edea of the idea of Garden and SeeD that she will create. Later on he is able to properly recollect his memories and thus return to the present with the help of Rinoa. The end cinematics is of when Squall returns back to the present. Seifer no longer a member of Garden, reunites with his friends Raijin and Fuji; Laguna visits Raine’s grave (in remembrance of his proposal to her) along with Ellone, Ward and Kiros; and a huge celebration takes place in the Garden with Squall and Rinoa sharing a kiss.
