We flew a prototype of the Nuclear Compton Telescope (NCT) on a high altitude balloon from Fort Sumner, New Mexico on 2005 June 1. The NCT prototype is a soft gamma-ray (0.2-15 MeV) telescope designed to study, through spectroscopy, imaging, and timing, astrophysical sources of nuclear line emission and gamma-ray polarization. Our program is designed to develop and test the technologies and analysis techniques crucial for the Advanced Compton Telescope satellite, while studying gamma-ray radiation with very high spectral resolution, moderate angular resolution, and high sensitivity. The NCT prototype utilizes two, 3D imaging germanium detectors (GeDs) in a novel, ultra-compact design optimized for nuclear line emission (0.5-2 MeV) and polarization in the 0.2-0.5 MeV range. Our prototype flight was a critical test of the novel instrument technologies, analysis techniques, and background rejection procedures we have developed for high resolution Compton telescopes.