The reactor operates by converting organic analytes after GC separation into methane before detection by FID. The oxidation and reduction reactions occur sequentially, wherein the organic compound is first combusted into molecules of carbon dioxide, which are subsequently reduced to methane molecules. The following reactions demonstrate the combustion/reduction process for formic acid. 
HCOH + 0.5O   ↔   CO + HO
CO + 4H   ↔   CH + 2HO
The reactions are faster compared to the time scales of typical chromatography, resulting in manageable peak broadening and tailing. Elements other than carbon are not ionized in the hydrogen and oxygen flames of the FID and thus do not contribute to the FID signal.