En route to their first hire as full-fledged SeeD mercenaries, Squall, Zell and Selphie are rendered unconscious by a mysterious force and their essences are transported to the past. There, a bumbling yet stout-hearted officer of the Galbadian Army, Laguna Loire, and his two companions, Kiros Seagill and Ward Zabac, are lost in dense woods that would later be known as Timber. They find a transport in a clearing, and evacuate to the Galbadian capital of Deling City.
Laguna and friends drown their sorrows at the Deling City Hotel bar, where a budding musician named Julia Heartilly catches Laguna's eye. He's had a crush on her ever since she came to Deling, but is too nervous to act on it. He starts cramping up and stuttering even as Kiros and Ward cheer him on. Julia doesn't mind and invites him to her room. The two hit it off, but Laguna gets lost in his fantastical life story and knocks himself out to sleep. From then on, he doesn't see Julia again.
Back in the present, the SeeDs come to, believing that what happened was a crazy dream. They brush it off, deboarding their train at Timber, where the Forest Owls give them their assignment: help the resistance in any way they can. Their first task is to intercept President Vinzer Deling, who is said to be arriving by train. The Owls hatch a plot to have the SeeDs foil Galbadian security with a dummy President Deling while the Owls presumably corner him. The plan goes awry when the President is discovered to be a decoy himself, and turns out to be the shape-shifting zombie Gerogero, whom they defeat.
The SeeDs escape the city with lead Owl Rinoa in tow, and per Garden Code rules retreat to Galbadia Garden, only to find themselves knocked out again in a small forest on the way there. This time, Laguna and his troops bumble their way through an old excavation site on the Centra continent, only to be cornered by Esthar forces. Though they use a number of traps to stymie their pursuers, their relief doesn't last long. A final confrontation takes place at the top of the site. Wounded, Laguna, Kiros, and Ward jump from the cliff...
In the midst of a failed assassination plot, Squall and friends are captured and sent to D-District Prison where they again are knocked out. Back in the past, Laguna and Kiros were taken into the village of Winhill, where they return the citizens' kindness by fending off monsters. Julia has died in a car crash, but not before meeting and marrying Galbadian general Fury Caraway and composing a tribute to her lost love, "Eyes on Me". Ward, meanwhile, is scrubbing the decks of D-District Prison as a janitor. In Winhill, Laguna meets up with a bartender named Raine and her adoptive daughter Ellone, whom he is told must be protected at any cost. He raises Ellone as his own, along with Raine. The Estharians soon find and capture her, bringing her to the advanced techno-city to unlock her secrets. Laguna is left to wander the world as a journalist, ever in search of Ellone; Raine dies after the birth of her second child, who becomes an orphan.
The SeeDs make a bold escape from prison with Rinoa's help, defeating Biggs and Wedge along with Galbadian war droids, and head into the events of the Balamb Garden Revolt, quelling an insurrection led by Master NORG and rendering the Garden mobile. After a dangerous detour at Fishermans Horizon involving G-Army forces, the SeeDs engage in the Battle of the Gardens, where they confront and defeat the possessed Edea Kramer, to be knocked out a fourth time. Ellone reveals that she is the one responsible for these episodes, and the party experiences a dream of Laguna at the Vienne Mountains, doing a side job starring in a film, which goes bust when a live Ruby Dragon wanders onto the set. Spooked though he is, Laguna defeats the beast, Later, he and his friends make the journey to Esthar, where he succeeds in trapping the sorceress Adel, Esthar's leader, and rescues Ellone.