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