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For the first time, the calculation of the nuclear matrix element of the double-$β$ decay of $^{100}$Mo, with and without the emission of two neutrinos, is performed in the framework of the nuclear shell model. This task is accomplished starting from a realistic nucleon-nucleon potential, then the effective shell-model Hamiltonian and decay operators are derived within the many-body perturbation theory. The exotic features which characterize the structure of Mo isotopes -- such as shape coexistence and triaxiality softness -- push the shell-model computational problem beyond its present limits, making it necessary to truncate the model space. This has been done with the goal to preserve as much as possible the role of the rejected degrees of freedom in an effective approach that has been introduced and tested in previous studies. This procedure is grounded on the analysis of the effective single-particle energies of a large-scale shell-model Hamiltonian, that leads to a truncation of the number of the orbitals belonging to the model space. Then, the original Hamiltonian generates a new one by way of a unitary transformation onto the reduced model space, to retain effectively the role of the excluded single-particle orbitals. The predictivity of our calculation of the nuclear matrix element for the neutrinoless double-$β$ decay of $^{100}$Mo is supported by the comparison with experiment of the calculated spectra, electromagnetic transition strengths, Gamow-Teller transition strengths and the two-neutrino double-beta nuclear matrix elements.