Smaller size and better performance of computing devices, sensors and actuators provide new opportunities for intellectual control in complex mechatronic systems in the transition process and in the turbulent environment. Previously, problems of control in changing environment and environment with time-varying state structure were not studied properly due to technical constraints. Change of the state structure is possible with the active interaction with the outer world. In this paper we show how self organization of the complex system can be used for adaptation to change of the state structure. As an example we consider an airplane with an array of ``feathers'' with sensors and actuators on the surface of its wing. The goal of the system is leveling the perturbing forces in the turbulence and converting the airflow into the laminar flow with the multi-agent protocol. Applicability of this approach is illustrated by simulation.