I watched the Matrix movies, and the explanation given for Neo flying and having super-strength and telekinesis is that the Matrix isn't real, and it can be hacked/modded. How does Neo have powers in the simulated reality of the Matrix? I don't understand how Neo could do whatever he wants in the Matrix. Plus, his stamina is finite, which doesn't make sense to me since it is a computer simulation. How do Neo's powers work in the matrix in the matrix movies?
Neo is The One, and has superhuman abilities due to his connection to the Source. This is explained (poorly) when he meets The Architect. According to fandom:
One significant anomaly appeared two-thirds into the Matrix's first cycle. A human was imbued with control of additional Matrix programming, and an instrinsic, metaphysical conceptulisation of the Matrix that was derived from the Source.