Disc One
The game begins when, following a training fight with classmate Seifer Almasy, SeeD cadet Squall Leonhart awakens in the infirmary. He is reminded that he must go to the nearby Fire Cavern in order to finish his preliminary training before the start of the final SeeD exam. On his way to meet his instructor,Quistis Trepe, Squall (literally) runs into Selphie Tilmitt a new exchange student from Trabia Garden. She asks him for a brief tour of Balamb Garden, after which she leaves him to proceed to the Fire Cavern, where he beats and obtains the GF Ifrit.
Upon returning to Garden, Squall prepares for the Final SeeD exam; to assist in the Dollet Dukedom which is under invasion by Galbadian soldiers. He is assigned to a squad with fellow cadet Zell Dincht with his rival Seifer as squad leader. During the mission, Seifer abandons his squad and Selphie Tilmitt joins them, revealing she too is taking part in the exam. Upon returning, Squall, Selphie, and Zell graduate as SeeD, while Seifer fails the exam due to his poor conduct.
At the graduation ball that evening, Squall encounters a beautiful young girl, with whom he dances but does not learn her name. The next day, Squall, Zell and Selphie are sent on their first mission to Timber to assist the resistance group The Forest Owls.
On the way to the mission, all three characters pass out and upon waking they discover that they all experienced the same dream, about three Galbadian soldiers: Laguna Loire, Kiros Seagill, and Ward Zabac. Despite the strange incident, they dismiss it and continue with their mission.
They meet with the Forest Owls, the leader of which turns out to be the girl Squall danced with - Rinoa Heartilly. After failing to kidnap the President of Deling, the group witness a TV broadcast announcing the Sorceress Edea as the new leader of Galbadia. At this point Seifer attempts to kill the president and then agrees to join Sorceress Edea, though the party is led to believe Seifer has been executed.
The party is then contracted to assassinate the Sorceress in Deling city during her parade (with the help of expert sharpshooter Irvine Kinneas) and work alongside the Galbadian Military General, Caraway. During the mission, the team discovers that Seifer is alive and is now the working as Edea's knight. The assassination fails and Squall, Irvine, and Rinoa attack Seifer and Edea head on. Squall is struck down by Edea's final blow,and the rest of the party find themselves in the District prison.
 Disc Two
Sqaull and Irvine are back in the dream world at the start as Laguna and Kiros. After the previous events, Laguna is in Winhill at a house when a little girl called Ellone tells him a man dressed funny is talking with Raine. After Laguna goes to Raine he meets back up with Kiros and then they go patrol the city for monsters. On their return they see Raine and Ellone talking about Laguna and what they are going to do about him, which prompts Laguna to go back to his house and hopes he will still be there when he wakes up.
Squall wakes up in the D-District Prison and then is interrogated by Seifer, while Quistis, Zell, Rinoa, and Selphie are in prison the guards call for Rinoa and then attack Zell after a trick by the guards Zell escapes from the cell and retrieves the weapons to which then they all escape looking for the rest of them. The party rescues Squall who learned during his interrogation that Edea is launching missile attacks at all of the Gardens. Irvine and Rinoa then return and they break out using Zell's idea he got from his dream. Once they are all out they drive in seperate ways: Squall and two others go to Balamb Garden and Selphie takes the other two to the Missile Base.
In the Missile Base, Selphie and her comrades disguise themselves as guards to run around in and they try and stop the missile before launch. After they stop it they realize they are too late and they are locked in while they set the self desturct to which the place got blown away.
At Balamb Garden, Squall and the other two make it there after hopping trains and find out the Garden is at war with itself. They being looking for Cid and when they find him he goes on about a protective project on the Garden which Squall insists he'll go get it to work after a run and a climb through an elevator he finds the machine sets it off which brings the Garden off the ground and escapes the missiles.
After the Garden is active the Garden NORG wants to see Squall and the other two which then explains about how Cid is worthless and then they engage in battle. Following this Cid calls for Squall and puts him in charge of the Garden, insisting they need a good leader and Squall is the best, to which then the Garden crashes into Fisherman's Horizon.
At Fisherman's Horizon, Squall and his two teamates are are on their way looking for the mayor. People welcome them with open in arms and insist they fix the Garden. After Squall explains the situation to the mayor and apologizes he then encounters the Galbadia soliders looking for a Ellone. After the mayor tells the party that there is no fighting in the town and that words can mean more, the mayor gets threatened by the soldiers before Squall leaps into action and takes them on. Then once again a machine called BGH251F2 comes back after defeaing it at the Missile base and Squall destroys the machine. The other party members with Selphie leap out and return back to the Garden.
Following this, Irvine then tells Squall that the repairs are being made and that he asked for help on something else which then Squall goes to sleep. Irvine then helps out on the Concert and open air concert by planning something special between Rinoa and Squall while he tries to get with Selphie so as they practice a recital for this plan Rinoa goes and gets Squall which Rinoa asks Squall about his feelings while the rest of the party perfrom.
While leaving Quistis informs Squall, Selphie needs rest and they hear that Balamb Graden is under siege! As Squall gets to Balamb soldiers are stopping people from entering the city as Zell comes to bust up the part Squall tells a lie to get into Balamb town. Squall and Zell then go around asking whats going on and realize they are not allowed out of the town or in the hotel so they rest in Zell's room. They go looking for a Commander after sveral questions they find him and its Raijin. After combat with him he then runs into the hotel and meets up with Fujin and they engage in a fight as well. After this fight Squall lets them go with no harm done and the Galbadia army retreat.
As Squall is back, Selphie insists on going to Trabia Garden to see the damage the missile made while there Selphie meets her old friends and tells Squall to meet at the Basketball court.
After all of them go to the court Selphie does a briefing on Trabia Garden and then they discuss what they are going to do next which then Irvine remembers something remarkable about the past and the reason none of them knew this was because of the GFs.
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