Eiji Shinjo, the main protagonist of the series, made his first appearance in Battle Arena Toshinden as an initially playable character and from then on appeared in all later games, including the spin-offs released only in Japan. He also makes a guest appearance in another fighting game published by Takara, D-Xhird, as a hidden, playable character.

Eiji is an adventurer who was trained in sword fighting, along with his friend Kayin Amoh, by his older brother Sho. However, Sho had suddenly abandoned the pair unexpectedly one day and since then, Eiji has been determined to find his older brother. Eiji had entered the first two Toshinden tournaments in hopes of finding his lost brother. In the first tournament, Eiji found his brother and got defeated by him easily. In the second tournament, he encounters him again but this time...Sho barely defeats him. Despite these two losses, he managed to help destroy the Secret Society in the second game. Eiji then learned he was being targeted by the Organization and he entered the third tournament hosted by it. With the help of the fighters on his side, he managed to destroy the Organization and its leader Abel. Soon after, Sho finally faced Eiji one more time in a decisive battle and from within the end of the match, Sho had left his son Subaru in his care and it is implied that Eiji won this time. However, before Eiji had a chance to fully reunite with his brother, Sho had disappeared immediately afterwards once again and Sho hasn't been heard from since.

For the next few years, Eiji had trained Subaru in sword fighting and eventually passed down his katana to him. Eiji was then offered to become the leader of a newly reformed Secret Society. He accepted, hoping to turn the long corrupted organization's power to good.

With the help of the imprisoned altered humans Eos and Zero, Eiji had hosted and participated in the fourth tournament to gather the Four Sacred Arms; powerful, mystical weapons based on the Four Symbols of the Chinese constellations. During the tournament, Eiji was given the chance to battle against his nephew Subaru in hopes to see on how his fighting ability had progressed from within time itself. Though Eiji was happy to know that Subaru's fighting skill was almost identical to himself and Sho's, he couldn't afford to lose focus on his real task, which was to confront his long-time enemy Vermilion and battle against him for the possession of the Four Sacred Arms. The outcome of this fight remains a mystery, but it is likely that Eiji may have killed Vermilion and saved the world from total destruction.