The Sea Emperor dies due to old age. The creature is 2600 years old, and according to the PDA, it has massively outlived its average lifespan. It is heavily implied that the Sea Emperor has continued to live for such a long time to ensure its babies will hatch and live on. Also, it has used all its strength to live long and ensure that the planet continues to receive Enzyme 42 from it, which is a cure for the Khaara virus. Since the babies have hatched, there are now new creatures capable of producing the cure.