The kingdoms of Clarence and Garla are at war with each other. The priestess Mirelia leads a group of children refugees through a forest, and is attacked by Garlan troops. Guy, a Garlan officer, doubts the methods of his superior, general Neston, and helps Mirelia and the kids escape. On their way they meet other heroes who are willing to protect the children and together resist the Garlan invasion.
Nana Eiyū Monogatari II is not directly connected to its predecessor story-wise, but has a nearly identical gameplay system: the game consists out of a series of tactical battles, with characters leveling up in a RPG fashion after a set number of attacks. Like in the previous game, the system is very simple, without inventory, equipment, or multiple attacks available. The sequel has more battles and more diverse goals, which often involve more than simply eliminating all the enemies and require the player to protect children from being harmed, rescue innocent people, pursue fleeing enemies, etc.