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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for coronavirus disease-19 (COVID-19). This virus has caused a global pandemic, marked by several mutations leading to multiple waves of infection. This paper proposes a comprehensive and integrative mathematical approach to the third wave of COVID-19 (Omicron) in the Kingdom of Saudi Arabia (KSA) for the period between 16 December 2022 and 8 February 2023. It may help to implement a better response in the next waves. For this purpose, in this article, we generate a new mathematical transmission model for coronavirus, particularly during the third wave in the KSA caused by the Omicron variant, factoring in the impact of vaccination. We developed this model using a fractal-fractional derivative approach. It categorizes the total population into six segments: susceptible, vaccinated, exposed, asymptomatic infected, symptomatic infected, and recovered individuals. The conventional least-squares method is used for estimating the model parameters. The Perov fixed point theorem is utilized to demonstrate the solution's uniqueness and existence. Moreover, we investigate the Ulam–Hyers stability of this fractal–fractional model. Our numerical approach involves a two-step Newton polynomial approximation. We present simulation results that vary according to the fractional orders (γ) and fractal dimensions (θ), providing detailed analysis and discussion. Our graphical analysis shows that the fractal-fractional derivative model offers more biologically realistic results than traditional integer-order and other fractional models. [ABSTRACT FROM AUTHOR]