The calibration pipeline of the level zero images obtained from the Magneto-Optical filters at Two Heights (MOTH II) instrument is presented. MOTH II consists of two 20 cm aperture instruments, each using a Magneto-Optical Filter (MOF): one at 5896 Å (Na D2-line), the other one at 7700 Å (K I-line). MOTH II instruments thus provide full disk line-of-sight Doppler velocity and magnetic field measurements at two heights in the solar atmosphere. The developed MOTH II pipeline employs a set of standard calibration corrections, a correction for signal leakage, due to the non-ideal behavior of the polarizers, and the geometrical registration between the eight images acquired by four CMOS cameras, relative to two components of the signal in two circular polarization states, in each of the two channels. MOTH II data are used to investigate atmospheric dynamics (e.g., internal gravity waves and magneto-acoustic portals) and Space Weather phenomena. Particularly, flare forecasting algorithms, based on the detection of magnetic active regions (ARs) and associated flare probability estimation, are currently under development. The possible matching of MOTH II data with SDO/HMI and SDO/AIA images into a flux rope model, developed in collaboration between Harvard-Smithsonian CfA and MIT Laboratory for Nuclear Science, is being tested.