Methods and systems include supplying pulsed microwave radiation through a waveguide, where the microwave radiation propagates in a direction along the waveguide. A pressure within the waveguide is at least 0.1 atmosphere. A supply gas is provided at a first location along a length of the waveguide, a majority of the supply gas flowing in the direction of the microwave radiation propagation. A plasma is generated in the supply gas, and a process gas is added into the waveguide at a second location downstream from the first location. A majority of the process gas flows in the direction of the microwave propagation at a rate greater than 5 slm. An average energy of the plasma is controlled to convert the process gas into separated components, by controlling at least one of a pulsing frequency of the pulsed microwave radiation, and a duty cycle of the pulsed microwave radiation.