Energy can be stored in different forms.
Just like burning wood gives off heat energy but the wood is converted to carbon dioxide, water and ashes. The energy is released from chemical bonds – the matter is still there but in different forms.
Same thing happens with food we eat. It is basically (simplifying all the complicated processes) a slow burning process. The food is converted to sugars which react with the oxygen (why we need to breathe) and release energy. It isn’t literally burning but the chemical reaction is similar.
Nuclear energy converts very little matter to energy. It is mostly one kind of element transforming into another element and releasing energy. A little bit of mass is converted to energy but the bulk of the matter remains. Only something like anti-matter and matter reactions can convert nearly all matter to energy – but that really happens only in research labs and in very very very small quantities.
Using the example of our sun (a typical star). By the end of its life, it is estimated that it will convert way less than 1% of its mass to energy. The bulk of the matter will remain as different elements.
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