The $\textit{BABAR}$ Collaboration data of the $D^0 \to K^0_S K^+ K^-$ process are analyzed within a quasi two-body factorization framework. In earlier studies, assuming $D^0$ transitions to two kaons and the transitions between one kaon and two kaons to proceed through the dominant intermediate resonances, we approximated them as being proportional to the kaon form factors. To obtain good fits, one has to multiply the scalar-kaon form factors, derived from unitary relativistic coupled-channel models or in a dispersion relation approach, by phenomenological energy-dependent functions. The final state kaon-kaon interactions in the $S$-, $P$- and $D$- waves are taken into account. All $S$-wave channels are treated in a unitary way. The $K^+K^-$ and $\bar K^0 K^+$ $S$-wave effective mass squared distributions, corrected for phase space, are shown, in a model-independent manner, to be significantly different. Then the $f_0(980)$ resonance must be included at variance with the BABAR analysis. The best fit has 19 free parameters and indicates i) the dominance of annihilation amplitudes, ii) a large dominance of the $f_0(980)$ meson in the near threshold $K^+K^-$ invariant mass distribution and iii) a sizable branching fraction to the $K_S^0 \ [\rho(770)^+ + \rho(1450)^+ + \rho(1700)^+] $ final states. An appendix provides an update of the determination of the isoscalar-scalar meson-meson amplitudes based on an enlarged set of data. A second appendix proposes two alternative fits based on scalar-kaon form factors calculated from the Muskhelishvili-Omn\`es dispersion relation approach. These fits have $\chi^2$ quite close to that of the best fit but they show important contributions from both the $f_0$ and $a_0^0$ mesons and a weaker role of the $\rho^+$ mesons.
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