A robust and computationally efficient "Versatile Transition Prediction Methodology" (VTPM) for hypersonic boundary layers is developed, verified and validated. VTPMis based on two approaches: (1) A frequency domain linearized Navier-Stokes solver (VTPM-FD), and (2) an adaptive mesh-refinement wave-packet tracking technique (VTPM-WPT). Both approaches build on the governing equations in their most general form such that all relevant transition mechanisms can be accounted for, e.g. receptivity, convective and absolute instabilities for 3D baseflows, transient growth, crossflow instability, and secondary instability. Both approaches allow for fully three-dimensional flows as encountered for arbitrary complex geometries, and does not require structured grids and pre-defined disturbance marching paths as required for current state-of-the-art PSE based methods. The VTPM framework allows to connect the different transition stages in a consistent fashion, such that the entire transition process can ultimately be predicted solely based on information about the environmental disturbances. Therefore, VTPM will allow a physics-based extrapolation of ground test measurements to free-flight conditions. VTPM can also be directly imported into the transition prediction amplitude method developed by Marineau et al. The software package is developed from the ground up such that the final product will be readily accessible for "non-expert" users.