After completing his doctorate, Stuart worked as a Research Fellow at the Japan Atomic Energy Research Institute. During this time, he studied the overlap of q=2 islands in reversed shear discharges in the JT60-U tokamak. After Japan, Stuart was employed as a Research Fellow at the Center for Plasma Theory and Computation in the Department of Engineering Physics at the University of Wisconsin -- Madison, where he began studying the theory of ballooning modes in stellarators, particularly helically symmetric stellarators such as HSX in operation at Madison. A computational code implementing theory regarding the effect of profile variations on ballooning stability was developed.

In 1999, Stuart came to Princeton and became involved with the National Compact Stellarator Design (NCSX) . Techniques to eliminate magnetic islands in full-pressure stellarator designs, both fixed and free boundary, were developed and applied to NCSX. This work lead to the development of an stellarator optimization algorithm that incorporates flux surface quality, ideal stability and engineering constraints.

Since then, Stuart has continued to study some topics in ballooning stability, and more recently has returned to the study of chaotic magnetic fields. Topics of present study include the transport of heat and particles in chaotic magnetic fields and, in collaboration with Prof. Dewar, the construction of an MHD equilibrium code that is consistent with the ideal MHD and the structure of chaotic magnetic fields.