Here is the full list of all 16 Ys VI: The Ark of Napishtim achievements. It takes around 15-20 hours to unlock all of the achievements on Windows.
Complete the game on Nightmare difficulty.
Obtain every other achievement.
Win a boss fight with 1 HP remaining.
Defeat Majuunun.
Acquire every Tabulas.
Complete the game in Catastrophe Mode.
Complete Boss Rush mode on any difficulty.
Win the duel with Geis.
Destroy the Ark’s Central Shaft.
Defeat Ernst.
Acquire all equipment.
Win a boss fight without taking a single hit.
Defeat Orjugan.
Defeat Ud-Meiyu.
Defeat Zonplas.
Defeat the Wandering Calamity.