The walkthrough for Secret of Mana is split up sequentially by the designated chapters in the game. Optional boss encounters and sidequests are listed in each chapter as they are best attempted.

Using the power of Mana, a civilization had grown strong... In time, Mana was used to create the ultimate weapon: the Mana Fortress... This angered the gods. They sent their beasts to destroy the Fortress... A violent war rocked the world, and Mana seemed to disappear... Before all was lost, a hero with the Mana Sword smashed the Fortress... Though the civilization had been destroyed, the world was peaceful again. But time flows like a river... and history repeats...

1. Potos Falls and Potos Village
2. Water Palace and Pandora
3. Gaia's Navel
4. Witch Elinee
5. The Underground Palace
6. Pandora Ruins
7. Thieves' Ship
8. Upper Lands
9. Dragon Caves
10. Kakkara Desert
11. Ice Country
12. Fire Palace
13. The Empire
14. Imperial Castle
15. The Palace of Darkness
16. Gold City
17. True Courage
18. Sunken Continent
19. Grand Palace
20. Pure Land
21. Mana Fortress