Embodiments of the present disclosure relate to a memory system, a memory controller, and a method of operating the memory system. According to the embodiments of the present disclosure, when result data obtained by derandomizing data included in a flag area is different from reference data after a random data unit is derandomized based on a seed, it is possible to detect an error occurring in the seed in a process of derandomizing the data and to prevent malfunction of firmware in advance by searching for a target seed and derandomizing the random data unit based on the target seed.