Where does the Excess current produced in a alternator charging system goes?

The excess current produced in an alternator charging system is diverted to the battery for storage. If the battery reaches or nears its fully charged state, the voltage regulation in the alternator will reduce the excitation magnetic field to maintain steady output, preventing damage to the electrical system. Any leftover surplus power gets dissipated by various electrical components' parasitic draws or lost as heat within the alternator due to increased internal resistance to limit excessive electrical flow within the circuit.