Abstract The mission of the low aspect ratio spherical tokamak NSTX-U is to advance the physics basis and technical solutions required for optimizing the configuration of next-step steady-state tokamak fusion devices. NSTX-U will ultimately operate at up to 2 MA of plasma current and 1 T toroidal field on axis for 5 s, and has available up to 15 MW of neutral beam injection power at different tangency radii and 6 MW of high harmonic fast wave heating. With these capabilities NSTX-U will develop the physics understanding and control tools to ramp-up and sustain high performance fully non-inductive plasmas with large bootstrap fraction and enhanced confinement enabled via the low aspect ratio, high beta configuration. With its unique capabilities, NSTX-U research also supports ITER and other critical fusion development needs. Super-Alfvénic ions in beam-heated NSTX-U plasmas access energetic particle (EP) parameter space that is relevant for both α-heated conventional and low aspect ratio burning plasmas. NSTX-U can also generate very large target heat fluxes to test conventional and innovative plasma exhaust and plasma facing component solutions. This paper summarizes recent analysis, theory and modelling progress to advance the tokamak physics basis in the areas of macrostability and 3D fields, EP stability and fast ion transport, thermal transport and pedestal structure, boundary and plasma material interaction, RF heating, scenario optimization and real-time control.