is set in IS 475, roughly 16 in-game years after the events of Suikoden II. The game takes place in the diverse Grasslands region, an area to the northwest of Dunan from Suikoden II (which itself was to the north of the Toran area from Suikoden). Politically, the Grasslands are mostly controlled by the Six Clans, a loose coalition between the Karaya, Lizard, Duck, Chisha, Safir, and Alma Kinan clans. The clans are considered rather backward and barbaric by neighboring powers, and the clans have comparatively smaller towns than the cities seen elsewhere in the Suikoden universe. On the western coast, the merchant nation of Zexen thrives. The Zexens were an ignored offshoot of Harmonia long ago, and have since grown to be powerful and independent. Their architecture, politics, and citizenry are similar to Renaissance Western European civilizations. To the east lie imposing mountains and eventually Harmonia, a gigantic and populous nation. Harmonia maintains outposts along the border, notably the submissive, conquered town of Le Buque and the trading citadel Caleria.
The Trinity Sight System contains three chronological chapters per character. Players have the ability to switch characters and point of view after the end of each chapter.
Hugo is the son of Lucia, the chief of the Karaya Clan. He is sent to visit the Zexen capital to deliver a truce offer for the Clans, who had been clashing against Zexen recently. The visit goes wrong, and Hugo is forced to flee back to Karaya, only to find it in flames. His childhood friend, Lulu, is then slain by Chris Lightfellow. Eager for revenge and to help defend the Clans, Hugo travels the Grasslands, eventually reuniting with the other Karayans in exile at the Lizard Clan's Great Hollow. He learns from Lilly Pendragon of the Flame Champion's story, and eventually seeks out the Flame Champion for aid with the Clans set upon by both the Zexens and, in Chisha village, the Harmonians.
Chris Lightfellow is the Acting Captain of the Zexen Knights. Respected and revered as a hero, she is known as the 'Silver Maiden'. While she is dedicated to protecting her country and people, Chris finds herself increasingly frustrated with the Zexen Council, disagreeing with their methods. This dilemma only worsens as the conflict with the Grassland clans increases.
Chris commands the Zexen forces against the Grassland clans early in the game, fighting them at the botched truce agreement, the Karaya village (where she kills Hugo's friend Lulu), and the Lizard's Great Hollow. At Iksay Village, where she helps fend off a combined assault by the Lizard and Karaya clans, she finds that her missing and assumed dead father Wyatt may still be alive. She sets off on a personal journey throughout the Grasslands to find him and whatever traces she can as to the nature of recent events. In doing so, Chris also comes to meet and learn more of the people she has been fighting.
Geddoe is the reserved and enigmatic leader of the Twelfth Harmonian Southern Fringe Defense Force Unit, a band of mercenaries under the employ of Harmonia. He is charged with investigating rumors of the resurgence of the Fire Bringer. As a somewhat neutral observer on the Zexen - Grassland conflict, Geddoe and his band see several of the more provocative moments, such as the inexplicable attack by the Zexens on the Great Hollow, the assassination of the Lizard clan chief, and the burning of Karaya village by the Zexens. Despite Harmonia's orders, Geddoe has his own agenda; he is especially suspicious of a new bishop of Harmonia who always wears a mask.
Eventually Geddoe is ordered to look for the True Fire Rune itself, a rather easy task for him. Geddoe is in truth the bearer of the True Lightning Rune and was a personal companion of the Flame Champion from 50 years ago. He travels to the True Fire Rune in order to defend the Grasslands once more.
Despite his knowledge of history and events, Geddoe does not often divulge his information, preferring to remain enigmatic. Likewise, the members of his team have generally left their pasts behind and use aliases. Geddoe's chapters are also somewhat unique in that his team changes very little; after saving and recruiting the Karayan Aila, Geddoe's 5 companions stick together, unlike the other chapters in which characters join and leave often.