This dataset provides O2/N2, CO2, Ar/N2, and stable isotope ratios of CO2 measured in flasks collected by the Medusa Whole Air Sampler during airborne campaigns conducted by NASA's Atmospheric Tomography (ATom) mission. ATom deployed an extensive gas and aerosol payload on the NASA DC-8 aircraft for a systematic, global-scale sampling of the atmosphere, profiling continuously from 0.2 to 12 km altitude. Flights occurred in each of 4 seasons from 2016 to 2018. Medusa collected 32 cryogenically dried, flow, and pressure-controlled samples per flight. The samples are collected by an automated sampler into 1.5 L glass flasks that integrate over 25 seconds. Medusa provides discretely-sampled comparisons for onboard in situ O2/N2 ratio and CO2 measurements and unique measurements of Ar/N2 and 13C, 14C, and 18O isotopologues of CO2. Medusa flasks are analyzed on a sector-magnet mass spectrometer and a LiCor non-dispersive infrared CO2 analyzer by the Scripps O2 Program at Scripps Institution of Oceanography.