12 years ago, a lone foreign ship was attacked off the coast of Japan by the forces of warlord Oda Nobunaga. There were only two survivors, discovered by a ninja master named Kageha: an injured sailor named John, and his 3-year-old son. The sailor told Kageha with his dying breath that his ship had been attacked by Nobunaga, and the ninja master took the child as his disciple, training him in the ways of the ninja, and giving him the name Burai. Now, the young ninja sets out with his companions to have revenge on the evil warlord Nobunaga.

Ninja Burai Densetsu is a turn-based strategy game similar to Fire Emblem or Langrisser set in Sengoku-period Japan. The player takes turns with the computer, positioning individual units on the grid-based map, and attacking enemies. Units can also visit towns to purchase new equipment or recovery items; not just the player, but enemies may also flee to nearby towns when attacked. Each stage has a specific goal and a strict time limit, measured in days. Short scenes between stages move the story forward.