Methods and systems are provided to deliver a neural stimulation therapy to treat apnea episodes. The methods and systems detect a respiratory pattern of a patient and identify a type associated with the respiratory pattern. A sleep stage is detected that the patient is experiencing and the method and system identify when the sleep stage warrants therapy. When the respiratory pattern corresponds to an apnea episode (AE) and the sleep stage warrants therapy, the methods and systems deliver an apnea episode terminating neuro-stimulation (AET-NS) therapy configured to terminate the AE. A type of AE therapy that is delivered may be based on the sleep stage that was detected. The methods and systems may determine whether the AET-NS therapy successfully terminated the AE, and, if not, adjust the AET-NS therapy and deliver a new AET-NS therapy.