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With space more accessible than ever, academic institutions like the University of Colorado (CU) Boulder have exhibited that CubeSats (compact, homogeneous, rectangular satellites with masses below 14 [kg]) can be leveraged for remarkable space missions capable of making significant advances to both scientific and technological fields. One such CubeSat project is the NSF-funded Space Weather Atmospheric Reconfigurable Multiscale Experiment (SWARM-EX), which will launch three 3U CubeSats into a “swarm” that will demonstrate autonomous formation flying capabilities while simultaneously studying the spatial and temporal variability of ion-neutral interactions in the equatorial Ionosphere-Thermosphere region. Although the small stature of CubeSats and their standardized deployer options help to lower unit development cost and facilitate launch opportunities, the physical size limits of CubeSats prove to be a double-edged sword vis-à-vis sustaining a stable power state while hosting instruments with high power demands and often strict pointing requirements. For SWARM-EX, this issue is magnified by the mission’s ambitious goals; to comply with mission requirements, a SWARM-EX spacecraft is required to concurrently (1) point the science instruments no more than 30° off ram when they are operational, (2) point the GNSS patch antenna no more than 30° off zenith when the spacecraft are separated by ≤ 10 [km], (3) point the X-Band patch antenna no more than 18° off boresight from the ground station during downlink, (4) maximize the differential ballistic coefficient during differential drag maneuvers, and (5) maximize solar array power generation at all times. Consequently, advanced CubeSat Missions like SWARM-EX require innovative systems engineering solutions to remain power-positive during on-orbit operations. Through a combination of intricate pointing profiles, orbital simulations, a comprehensive and coordinated ConOps, battery state of charge simulation tools, and expertise from previous CubeSat missions, the SWARM-EX team has conceived a plan to successfully meet all these mission requirements; it is the aim of the authors to illuminate these strategies as a case study.