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 Boss Rush mode on any difficulty.
Obtain every other achievement.
Complete the game on Nightmare difficulty.
Complete the game in Catastrophe Mode.
Destroy the Ark’s Central Shaft.
Defeat Ernst.
Defeat Majuunun.
Win a boss fight with 1 HP remaining.
Acquire all equipment.
Acquire every Tabulas.
Defeat Orjugan.
Win a boss fight without taking a single hit.
Defeat Ud-Meiyu.
Defeat Zonplas.
Win the duel with Geis.
Defeat the Wandering Calamity.