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The story starts off with a SeeD cadet named Squall lying down in the infirmary recovering from a massive cut that was inflicted by Seifer, a fellow SeeD cadet and Squall's archrival. Squall's teacher, Quistis, helps Squall pass the rest of his requirements in order to take the SeeD exam later in the day. Squall is assigned to a team consisting of himself, Seifer, and Zell (a fighter and SeeD cadet). The team is dispatched to Dollet to stop the Galbadian soldiers from invading Dollet. Once the team accomplished their goal, Seifer got frustrated due to the fact that there wasn't enough fighting. The team decided to go where the Galbadian soldiers were going, the Comm Tower. Just before going in, they met up with Selphie (SeeD cadet transferred from Trabia Garden). They completed their mission and went back to Balamb Garden (their home base). Squall, Zell, and Selphie passed the SeeD exam, but Seifer didn't. Later that night, the SeeD graduation party occurred. There, Squall met an astonishing woman who forced a dance with him. Before getting her name, she apparently found someone she was looking for and left. That night, Quistis confided in Squall that she will no longer be an instructor and that she might be working together with Squall.

The following day, Headmaster Cid (Dean of Balamb Garden) assigned Sqaull his first mission. Squall, Selphie, and Zell were sent to Timber to help a resistance faction called the "Timber Owls". To Squall's surprise, the girl that he danced with at the SeeD graduation was the leader of the Timber Owls and the reason she was in Garden was to get a deal with Headmaster Cid. It is learned that her name is Rinoa Heartilly. Their first mission was to kidnap and interrogate the president of Galbadia, which was a failure. They did learn from this that the real president was going to the T.V. station. Once Squall and company reached their, they watched the television as the president announced that Sorceress Edea was going to lead "peace talks" with Galbadia'a enemy. Obviously, Edea is really being sent so that the opposing countries would be intimidated by her. As the president delivers his speech, Seifer attacks the president but leaves after being persuaded by Edea to join her.

Squall, Quistis, Selphie, Zell, and Rinoa leave Timber to go to Galbadia Garden for assistance. Once arriving there, they learn that a joint venture between Balamb and Galbadia Gardens has been made. The two Garden's want to assassinate Edea during her parade in Deling City. The sniper is a sharpshooter named Irvine Kinneas. The 6 of them go to Deling city and meet with General Caraway, Rinoa's father, who will be leading the operation against the sorceress. The operation was going smoothly but Edea knew she was going to be shot at and blocked the bullet shot by Irvine. Squall then lead the head-on attack against the sorceress but was blocked off by Seifer. Squall beats Seifer but Edea immediately attacks and injures Squall, and she captures the rest of the group.