Joy Boy didn't lose the Ancient Kingdom's greatest power. He gave it up.
The Ancient Kingdom's greatest asset may have been a unique energy source that powered its otherwise impossible technology. Vegapunk cannot reproduce the original Ancient Energy and instead creates the Mother Flame, an incomplete modern substitute. Joy Boy may have recognized at the end of the Void Century that leaving the original energy intact would allow the catastrophe to continue, so he deliberately destroyed or sealed the source while preserving selected pieces of the ancient system for the future. This would explain why Emet, the Ancient Weapons, the Poneglyphs and other remnants survived while the Ancient Kingdom's original technological power did not. Eight hundred years later, Vegapunk unintentionally recreates a weaker substitute, allowing Imu to reactivate an Ancient Weapon and reproduce a small-scale version of the world-changing destruction that occurred during the Void Century. The final conflict may therefore be a struggle over whether the lost power should be recovered, controlled, possessed, or finally left free.
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