In this thesis we present phenomenological consequences of the modern nonperturbative regimes of String Theory, M- and F-Theory. The origins of SO(10) from M-Theory on G2 manifolds are discussed, accompanied by a detailed discussion on a rank-breaking mechanism and consequences for neutrino masses. The Minimal Supersymmetric Standard Model is derived from F-Theory compactifications exhibiting a spectral cover equation with Klein monodromy and a geometric parity that endows the spectrum with an effective matter parity. A dedicated and systematic study on R-Parity violating couplings in F-Theory is also presented, where we find these couplings to be generic, and we compute their magnitudes.