We report the discovery of a $\sim 1.5 \times 10^{-4}$ Hz ($\sim 2$ hr) X-ray quasi-periodic oscillation (QPO) in the active galaxy MS 2254.9-3712, using a $\sim 70$ ks XMM-Newton observation. The QPO is significantly detected ($\sim 3.3 σ$) in the $1.2 - 5.0$ keV band only, connecting its origin with the primary X-ray power-law continuum. We detect a highly coherent soft lag between the $0.3 - 0.7$ keV and $1.2 - 5.0$ keV energy bands at the QPO frequency and at a frequency band in a 3:2 ratio,...