The Kepler space telescope revealed new, unexpected phenomena in RR Lyrae stars: period doubling and the possible presence of additional modes. Identifying these modes is complicated because they blend in the rich features of the Fourier-spectrum. Our hydrodynamic calculations uncovered that a “hidden” mode, the 9th overtone is involved in the period doubling phenomenon. The period of the overtone changes by up to 10% compared to the linear value, indicating a very significant nonlinear period shift caused by its resonance with the fundamental mode. The observations also revealed weak peaks that may correspond to the first or second overtones. These additional modes are often coupled with period doubling. We investigated the possibilities and occurrences of mutual resonances between the fundamental mode and multiple overtones in our models. These theoretical findings can help interpreting the origin and nature of the “hidden” modes may be found in the high quality light curves of space observatories.