To meet the power demands of deep space missions to the outer reaches of the solar system and beyond, where solar energy is limited; designers have been searching for alternative means of power generation for space systems. Adequate power is needed for new investigations utilizing high capability instruments, concurrent scientific observation using multiple instruments, high-rate transmission of science data to Earth, and spacecraft propulsion. To address this issue, beginning 2002, NASA conducted a study to investigate the feasibility of using nuclear energy to power spacecraft. It was determined that a nuclear reactor based power plant could provide 100s of kilowatts of electrical energy that could then be used to meet the science and propulsion needs listed above. The conceptual spacecraft design consists of a nuclear reactor separated from the bus and instruments by a long boom to support large thermal radiator arrays and to provide attenuation of the reactor-generated radiation environment. During the cruise and the transition into and out of the orbit of each Icy moon, the electric power generated by the nuclear power plant will drive ion-based Electric Propulsion (EP) thrusters, located on two gimbaled pods, to propel the spacecraft. Additional electrical thrusters, Hall Thrusters, located on the pods or on the spacecraft bus will enable attitude maneuvering. Due to the nuclear reactor operating environment however, none of the thrusters are placed at the reactor end of the spacecraft. This geometry, and the fact that the spacecraft is very large and flexible, provides special challenges to the attitude control system engineers. Thrust Vectoring Control (TVC) will maintain the spacecraft attitude during the continuous low thrust period, but the interaction between the control system, navigation, and the structure has the potential to introduce undesired disturbances. This problem could be further exacerbated by the three body dynamics of the Jupiter moon environment. Analysis has shown that most scientifically interesting orbits are unstable and therefore require frequent orbit adjustment. Coupling between the ACS and navigation functions will complicate this problem and therefore would offer new challenges to both subsystems. Command and Data handling (C&DH) is another subsystem with unique issues and problems. One of the biggest challenges facing this subsystem is the unprecedented radiation environment in the Jovian system, particularly around Europa. The total ionizing dose (TID) behind 10 mil of aluminum accumulated over 113 days in orbit around Europa is predicted to be about 22 MRad. A second C&DH challenge would be accommodation of large data storage and transfer in a high radiation operating environment. The objective of this paper is to introduce the readers to some of the challenges facing the Attitude Control and Command and Data Handling subsystems, and give an overview of approaches being considered to deal with these challenges.