Abstract Previous X-ray works on Mrk 1239 have revealed a complex narrow-line Seyfert 1 that exhibits substantial absorption and strong emission from both collisionally ionized and photoionized plasmas. Here, we report on deep-pointed observations with XMM-Newton and NuSTAR, along with Swift monitoring, to understand the 0.3–30 keV continuum emission and the central engine geometry. A strong X-ray flare, where the AGN brightens by a factor of 5 in ∼30 ks, is captured between 4 and 30 keV and can be attributed to a brightening of the primary continuum. However, the lack of any variability below ∼3 keV on long or short timescales requires complete absorption of the AGN continuum with a neutral medium of column density ∼10^23.5 cm⁻². The timing and spectral properties are consistent with a blurred reflection interpretation for the primary emission. The variability and presence of a Compton hump disfavors ionized partial covering. The neutral absorber, if outflowing, could be crashing into the surrounding medium and interstellar medium to produce the low-energy continuum and collisionally ionized emission. Scattered emission off the inner torus could produce the photoionized emission. The intricate scenario is demanded by the data and highlights the complexity of the environment that is normally invisible when overwhelmed by the AGN continuum. Objects like Mrk 1239 serve as important sources for unveiling the interface between the AGN and host galaxy environments.