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ART$^2$ is a 3D multi-wavelength Monte Carlo radiative transfer (RT) code that couples continuum and emission lines to track the propagation of photons and their interactions with the interstellar medium (ISM). The previous version of ART$^2$, which included continuum and Ly$α$ line, has been extensively applied to hydrodynamics simulations to study multi-band properties of galaxies and ISM. Here, we describe new implementations of non-local thermodynamic equilibrium RT of molecular and atomic fine structure emission lines, and the parallelization of the code using a number of novel methods. The new ART$^2$ can efficiently and self-consistently produce a full spectrum that includes both continuum and lines such as [CII], [NII], [OIII], Ly$α$, and CO. These essential features, together with the multi-phase ISM model and the adaptive grid, make ART$^2$ a multi-purpose code to study multi-wavelength properties of a wide range of astrophysical systems from planetary disks to large-scale structures. To demonstrate the capability of the new ART$^2$, we applied it to two hydrodynamics simulations: the zoom-in Milky Way Simulation to obtain panchromatic properties of individual galaxies, and the large-scale IllustrisTNG100 Simulation to obtain global properties such as the line intensity mappings. These products are essential for a broad array of studies such as the correlations between physical and panchromatic properties and their evolution. By enabling direct comparison between numerical simulations and multi-band observations, ART$^2$ provides a crucial theoretical framework for the interpretations of existing observations, the plan for future surveys, and the synergy between multi-band galaxy surveys and line intensity mappings. Therefore, ART$^2$ is a powerful and versatile tool to bridge the gap between theories and observations of cosmic structures.