Ted, McDohl's best friend from Suikoden 1, has his profile picture hanging in McDohl's room in Gregminster.

Sheena's default equipment pays homage to his parents from Suikoden 1. His sword is called Kirinji like his father, Lepant, and he begins with an Earth Rune and permanently attached Star Earrings like his mother, Eileen.

If Jowy is hacked into the party during the game, neither the "King" version, or "Best Friend" version will appear in the HQ anywhere. They can both be removed and added to the party with unique (and different) dialogue, despite these never normally being accessible through traditional means. "Best Friend" Jowy can also be awarded the statue that appears at the top of the castle for obtaining the most kills, even though he is never a part of the party's team after the events that lead to the castle being accessible.

There are many unique dialogue choices for the end of the game after defeating the Beast Rune. Some of these require special conditions to be met, such as having only a single character with you.

Jowy and Nanami can also be hacked into the party using code, which will reveal Jowy having glitched text, but Nanami will have understandable dialogue.

If the player decides to run away Spoiler:with Nanami during the events that develop around Tinto, the player can reveal an alternate ending in which the hero and Nanami will live quietly in the country.

Additionally, many characters have unique dialogue during this scene, including a script coded in for both Viktor and Flik, even though there's no way for you to put them in your party at this point in the game.