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The Energy Cell is the Battery a Steward Construct gave to Link to power the Zonai Devices. When using a Zonai Device the HUD shows a battery slowly depleting as you use energy, if you power off the device or use it until it's empty it recharges slowly. but using it until it's empty will take slightly slower to recharge much like how your stamina works. You may upgrade your Energy Cell to have more batteries in order to power Zonai Devices longer. But it requires refining your Zonaite into Crystalized Zonai Charges and then refining 100 Crystalized Zonai Charges further to create a new Energy Cell at a Crystal Refinery.