A therapy system adapted to treat a patient's ventilatory instability using a ventilatory therapy, a gas modulation therapy, or both. The algorithm implemented by the therapy system monitors the ventilatory instability, such as Cheyne Stokes Respiration (CSR), mixed apneas, CPAP emergent apneas, and complex sleep disordered breathing (CSDB) and treats the ventilatory instability. The algorithm also determine a reference point with respect to the ventilatory instability. The therapy delivery system initiate the treatment based on the reference point.