An auxiliary control system, having a method for controlling same, controls subsea equipment such as a tree or manifold, for example, in the event of failure of a control umbilical. A power unit is installed subsea, and then a control tool is coupled to the subsea equipment. Control signals from topside source are transmitted to the power unit, which powers and controls the control tool in response to the control signals to operate a control element of the subsea equipment, such as a valve.