Suikoden tells the story of a nameless hero, known as Tir McDohl in the novelization, in the vein of a political-military oriented theme. Tir McDohl is the son of a Great General of the Scarlet Moon Empire, Teo McDohl. Teo is called away to fight a battle in the northlands, leaving his son alone under the guardianship of several family friends to begin his career in the Imperial Army. He soon comes to realise through his missions and association with his leaders that the corruption within the Empire's top tier has led to a country where its populace is enslaved and unhappy.
Through his friend Ted, he comes into possession of the Rune of Life and Death (also known as the Soul Eater), one of 27 True Runes that govern various aspects of the world. The Rune, ruthlessly hunted for by corrupt officials within the Empire and their manipulators, force Tir and his companions to flee the capital city of Gregminster.
This early chain of events forces Tir to cross paths with a rebel organisation where he is sheltered, although he is only convinced of the need to struggle against the Empire when the hideout is attacked and sacked by Imperial forces. Recruiting the help of Mathiu Silverberg, a former Imperial strategist, Tir's Toran Liberation Army starts off as a small force working to unite rebel factions throughout Scarlet Moon, and eventually becomes a force large enough and powerful enough to bring down the Empire itself.