The KOTO experiment at J-PARC searches for the rare decay, $K_L \rightarrow \pi^0\nu\overline{\nu}$. This search requires a high intensity $K_L$ beam, setting KOTO in a unique position to probe sub-GeV quark coupling to dark matter. One avenue to study this is the mode $K_L \rightarrow \pi^0\pi^0X$, where $X\rightarrow\gamma\gamma$. This mode was studied in the E391a experiment at KEK in the $X$ mass region 194.3-219.3 MeV, with the best upper limit on the branching ratio set with an $X$ mass of 214.3 MeV at $< 2.4 \times 10^{-7}$. In KOTO, with an improved calorimeter and kaon flux, the single event sensitivity is improved up to an order of magnitude in that mass range. In addition, the scope of the study is broadened to include the first search for $K_L \rightarrow \pi^0\pi^0X$ with $X$ mass in the range 160-190 MeV. The simulation results compared to data in the low mass region and preliminary Single Event Sensitivity (SES) will be discussed.