We study the gapped phase of Kitaev's honeycomb model (a $Z_2$ spin liquid) on a lattice with topological defects. We find that some dislocations and string defects carry unpaired Majorana fermions. Physical excitations associated with these defects are (complex) fermion modes made out of two (real) Majorana fermions connected by a $Z_2$ gauge string. The quantum state of these modes is robust against local noise and can be changed by winding a $Z_2$ vortex around one of the dislocations. The exact solution respects gauge invariance and reveals a crucial role of the gauge field in the physics of Majorana modes. To facilitate these theoretical developments, we recast the degenerate perturbation theory for spins in the language of Majorana fermions. ; Comment: 15 pages, 7 figures; added a brief history of twists, references, and clarified the count of the topological degeneracy of the ground state