We report on the destabilization of the mode-locking operation of a long cavity fiber laser. We show that the destabilization is accompanied by the abrupt emergence of a strong frequency-downshifted Stokes signal, and simultaneously, we find that the laser output displays characteristics typical of noise-like pulses. We use numerical simulations to illustrate how the Stokes signal grows from stimulated Raman scattering and plays a key role in the destabilization of the laser output. Our results indicate that stimulated Raman scattering may impose an ultimate limit on the energy scalability via cavity lengthening.