PROCYON is the first deep-space micro-spacecraft; it was developed at low cost and short time (about one year) by the University of Tokyo and JAXA, and was launched on December 3rd, 2014 as a secondary payload of the H II A launch of Hayabusa2. The mission primary objective is the technology demonstration of a microspacecraft bus for deepspace exploration; the second objectives are several engineering and science experiments, including an asteroid flyby. This paper presents PROCYON high-fidelity, very-low-Thrust trajectory design and implementation, subject to mission and operation constraints. Contingency plans during the first months of operations are also discussed. All trajectories are optimized in high-fidelity model with jTOP, a mission design tool first presented in this paper. Following the ion engine failure of March 2015, it was found the nominal asteroid could not be targeted if the failure was not resolved by mid-April. A new approach to compute attainable sets for low-Thrust trajectories is also presented.