Computational framework for non-Markovian multi-emitter dynamics beyond the single-excitation limit

While non-Markovian dynamics have been extensively studied in the single-excitation limit to predict non-trivial phenomena, this regime remains an idealization. Moving beyond it is essential, as optical nonlinearities and phase-error accumulation in multi-photon processes render the Markovian approximation fragile. In this work, we present a Green's function-based framework for modeling non-Markovian multi-emitter quantum electrodynamics within the two-excitation manifold. The modified Langevin noise (M-LN) formalism is employed for first-principles treatment of dissipative environments, while the emitter-centered mode (ECM) framework ensures computational tractability. Unlike conventional approaches that integrate out the reservoir, we construct a non-Markovian hierarchy of coupled differential equations by explicitly retaining photonic amplitudes. Within the two-excitation hierarchy, the formulation preserves total probability and retains phase information necessary to capture multi-photon interference. As numerical demonstrations, we investigate non-Markovian atom-field interactions in structured semi-infinite waveguide environments. We first consider a homogeneous waveguide as a baseline, observing enhanced Bell-state fidelity in selected configurations. Next, we examine collective decay of symmetric Dicke states in a waveguide with an embedded lossy dielectric slab, revealing selective stabilization and delayed excitation transfer induced by the structured reservoir. Finally, we analyze entanglement dynamics in the same setting, highlighting entanglement sudden birth and oscillatory revivals. In principle, the framework applies to arbitrary electromagnetic environments for which the dyadic Green's function can be obtained numerically, providing a versatile tool for investigating complex non-Markovian multi-photon phenomena beyond the single-excitation limit.