Recent advances in aerodynamic, structural, electronic, and propulsive technologies make possible a new generation of low-cost unmanned aircraft for atmospheric science research. The first such platform, designated Perseus, is already under development as a joint effort between Aurora Flight Sciences and Harvard University. Perseus' lithium battery propulsion system will enable it to carry a 50 kg chemical sampling payload to an altitude of 25km. The purpose of this SBIR program is to initiate development of a larger, more versatile follow-on platform called Theseus. The heart of the proposed Theseus platform is a solid polymer electrolyte fuel cell powering an electrically driven propeller. A unique oxidation scheme will allow Theseus to carry a 450 kg payload for thousands of kilometers at an altitude of 20-25 km, and to reach altitudes as high as 40 km for brief periods. The aircraft is intended to be operable by a field team of three people and to be transported in a single C-130. Due to the complete reusability of both the airframe and the payload/s, Theseus will be capable of performing almost all of the scientific missions currently flown on large balloons or the manned ER-2, at costs significantly lower than present. In addition, it will make possible a number of new missions due to its increased performance, precise spatial and temporal controllability, and increased operational flexibility.