Final answer:
The nurse should first remove secretions from the pharynx to ensure a clear airway and prevent respiratory distress during the newborn's second reactive period.
Step-by-step explanation:
During the second reactive period of a newborn, when the infant becomes more alert and there is an increase in mucus production and gagging, the nurse should prioritize ensuring the baby has a clear airway. Therefore, the correct initial intervention would be D. Remove secretions from the pharynx. This action helps to maintain a patent airway, allowing the newborn to breathe effectively. If mucus and secretions are not cleared, they can lead to respiratory distress, which is why this is the priority over other possible interventions listed.