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In this paper, a new structure of an autonomous system generating a valid flight scenario for a satellite is designed and implemented. The hypothetical mission of this satellite is imaging from any points which are specified by users and also acquiring a sequence of imaged from high priority points on earth like fires jungles or volcano. The main intelligent decision making system in the satellite has to generate flight scenario of a microsatellite by receiving longitude and latitude of each requested imaging point from the earth. In this article an introduction of intelligent systems and their architecture for a typical microsatellite, cooperation scenarios between ground stations and a satellite and their missions are investigated. Finally the proposed intelligent system architecture and implementation of each layer and their integration is discussed. To test this new developed architecture a proper test bench is designed too. One of the approaches is adding some degree of autonomy to OBC of a satellite. All goals that are mentioned for an intelligent system and expansion in autonomy lead to self-based decision making process. This onboard decision making process is helpful in those situations that are not previewed on earth therefore are not scheduled to be done by satellite. This facility helps the system to pass the unsafe situations and response to them in a best way. At least this aspect can reduce destructible side effects of sudden situations.