A breakthrough in neuroscience occurred when a technique was developed that allowed the precise control of neuronal activity using light. This technique, termed optogenetics, employs light-sensitive proteins, genetically introduced into neuronal cell membranes, to manipulate processes optically. Among the most widely used optogenetic tools is channelrhodopsin-2 (ChR2), a class of rhodopsin protein composed of seven transmembrane (TM) α helices, with a retinal Schiff base (RSB) moiety covalently bonded in an internal pocket. The protein exists as a dimer in the cell, which in turn leads to two RSB moieties (Fig. ). ChR2 functions as a light-gated ion channel: upon photon absorption, RSB undergoes a trans-cis isomerization, triggering the opening of a channel through the cell membrane. The high temporal precision makes channelrhodopsins useful tools for investigating neural circuits involved in memory formation, consolidation, and retrieval, and thus useful tools to better understand the brain, including cognitive decline during aging and neurodegenerative conditions such as Alzheimer's disease. Despite its advantages, in vivo optogenetic applications face challenges due to the scat-tering of visible light by biological tissue, which limits the penetration depth. Multiphoton absorption (MPA) provides a promising alternative by allowing the RSB moiety to be excited through the simultaneous absorption of multiple lower-energy photons. The use of longer wavelengths mitigates scattering effects, increases tissue penetration, enhances focality, reduces phototoxicity (thus reducing cell damage), and minimizes competition with hemoglobin. MPA cross-sections, which quantify the probabilities of absorption, are critical for understanding MPA processes. However, their experimental determination in biomolecules is complicated by factors such as uncertainties in determining protein concentration and the occurrence of spurious nonlinear optical processes. Reliable computational methods are therefore indispensable. Accurately modeling the spectra of rhodopsins requires thorough molecular dynamics (MD) sampling, as has been demonstrated in studies such as those conducted for bovine rhodopsin. Given that light absorption is a fundamentally quantum-mechanical (QM) process, it necessitates a QM description. However, the computational cost required to investigate transmembrane proteins at this level of theory remain prohibitively expensive. To address this chal- lenge, hybrid quantum mechanics/molecular mechanics (QM/MM) methods provide a practical and effective solution. Computational atomistic studies of ChR2 were hindered until its structure was resolved in 2017. Prior to this, classical molecular mechanics (MM) MD studies on the channel opening mechanism have primarily focused on C1C2, a chimeric structure combining ChR1 and ChR2. Once the ChR2 structure was resolved, nonadiabatic dynamics simulations provided insights into the RSB photoisomerization mechanism in both wild-type and mutant variants. Classical MM MD investigations have been conducted in conjunction with QM/MM MD force matching to study the initial steps of the pore opening and influx of water molecules. So far, all these investigations have been conducted assuming a single non-branched photocycle model. However, recent experiments in electrophysiology, timeresolved step-scan FTIR, and Raman spectroscopy reveal a unified two-photocycle model, a branched model with two open and two closed states. In addition to photoisomerization studies, computational research has investigated the effect of mutations on spectroscopic properties, such as variations in absorption wavelengths in bovine rhodopsin mutants, or the influence of mutations on C1C2 two-photon absorption cross sections. In this work, we propose a multiscale strategy to compute the one-, two-, and three-photon absorption spectra of ChR2, explicitly considering the lipid bilayer, transmembrane protein, and solvent environment throughout the workflow. We link spectral variations to structural differences in the two RSB moieties. To our knowledge, there has been no computational atomistic investigation on the MPA processes in ChR2.