This paper introduces a new fractional-order extended state observer (NFO-ESO) for guiding multi-agent systems through cluttered environments. The proposed agent model accounts for both external wind disturbances and internal unmodeled dynamics, treating them as a unified matched disturbance. By integrating the NFO-ESO, a robust distributed controller is developed to effectively manage these disturbances, enabling the agents to navigate through a virtual tube under perturbations. The NFO-ESO addresses the limitations of traditional ESO, which are typically effective only for low-frequency disturbances, by providing enhanced estimation capabilities for nonlinear and fast-varying disturbances. The proposed control strategy is validated via a simulation of multi-agent systems, addressing both wind interference and unmodeled dynamics.