The process of popping a kernel absorbs more energy than it releases. When there are still lots of un-popped kernels, so much heat energy is absorbed by all these kernels that it prevents the temperature of the oils and steam in the bag from rising to the point where an already popped kernel would burn. Once most of the kernels have popped, the heat energy has nowhere else to go and the temperature goes up, eventually burning the popped ones.
This is why it’s almost impossible to get all the kernels to pop without burning some of them.
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