We use a theoretical approach to reveal the electronic and structural properties of molybdenum impurities between MoS2 bilayers. We find that interstitial Mo impurities are able to reverse the well-known stability order of the pristine bilayer, because the most stable form of stacking changes from AA' (undoped) into AB' (doped). The occurrence of Mo impurities in different positions shows their split electronic levels in the energy gap, following octahedral and tetrahedral crystal fields. The energy stability is related to the accommodation of Mo impurities compacted in hollow sites between layers. Other less stable configurations for Mo dopants have larger interlayer distances and band gaps than those for the most stable stacking. Our findings suggest possible applications such as exciton trapping in layers around impurities, and the control of bilayer stacking by Mo impurities in the growth process.