Thunderstorms and lightning, typical mesoscale convective systems often cause severe flash floods and related disasters. The accompanying moderate to severe lightning also causes significant disruption. However, accurately simulating thunderstorms and lightning remains challenge for most mesoscale models, as they struggle to represent the mesoscale-convective processes that lead to thunderstorm formation. In this study, we analyzed a thunderstorm event that took place on 28th April 2015 in northeastern India using the Advanced Research version of the Weather Research and Forecasting (WRF-ARW) mesoscale model. This case was associated with extreme heavy precipitation events. We conducted a series of numerical experiments at a convection-permitting scale with a 3-km horizontal grid spacing using initial and boundary conditions (LBCs) from two sources, namely NCEP-GFS and NCEP-FNL. We also employed four microphysical schemes namely Thompson, WSM6, Morrison and Purdue Lin which are tested in WRFto evaluate the impact of the LBCs and microphysics schemes on the simulation of the thunderstorm event. This study highlights the critical role of experimental design in achieving realistic simulations of heavy precipitation events with the WRF model. It focuses on the evolution of thermodynamic and dynamical processes within an event. The results indicated that two microphysics schemes, namely the Purdue Lin and the WRF Single-moment 6-class schemes, performed better than other microphysics schemes in simulating this event, although with some variations in precipitation characteristics. Notably, the model simulation using NCEP-GFS LBCs and the Purdue Lin scheme produced a reasonable and realistic representation of the precipitation characteristics and associated dynamical and thermodynamic processes. Overall, this study underscores the importance of both microphysics schemes and LBCs in the simulation of thunderstorm events and emphasizes that the choice of microphysics scheme and the LBCs would substantially impact the accuracy and realism of thunderstorm simulations.