We introduce a hybrid many-body approach that combines the flexibility of the No-Core Shell Model (NCSM) with the efficiency of Multi-Configurational Perturbation Theory (MCPT) to compute ground- and excited-state energies in arbitrary open-shell nuclei in large model spaces. The NCSM in small model spaces is used to define a multi-determinantal reference state that contains the most important multi-particle multi-hole correlations and a subsequent second-order MCPT correction is used to capture additional correlation effects from a large model space. We apply this new ab initio approach for the calculation of ground-state and excitation energies of even and odd-mass carbon, oxygen, and fluorine isotopes and compare to large-scale NCSM calculations that are computationally much more expensive.