Short answer is that we don’t KNOW exactly, but there are a few theories.
One of the theories that make the most sense is that using specific brain/neural pathways (for example while doing a specific intensive task, or experiencing empathy), like any cellular usage, causes the buildup of metabolites, which degrades the functioning of those cells until the metabolites are cleared, just like how muscles can get fatigued, even if you have sufficient systemic energy.
Muscles have ample blood supply, and metabolites can be cleared fairly easily and quickly with rest. However, the brain needs sleep to efficiently clear the buildup of metabolites. So we effectively have a limit of how much we can do (well) in a day, mentally.
There are theories that suggest that it is the energy reserves in those brain cells that get depleted, but there is also evidence against that.
Other factors also play a role. Like for example you could developed a learned resentment for a person/situation after prolonged exposure, but that would be different from the physical fatigue it causes.
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