The National Spherical Torus Experiment (NSTX) is currently being upgraded to operate at twice the toroidal field and plasma current (up to 1T and 2MA), with a second, more tangentially aimed neutral beam (NB) for current and rotation control, allowing for pulse lengths up to 5s. Recent NSTX physics analyses have addressed topics that will allow NSTX-Upgrade to achieve the research goals critical to a Fusion Nuclear Science Facility. These include producing stable, 100% non-inductive operation in high-performance plasmas, assessing plasma-material interface (PMI) solutions to handle the high heat loads expected in the next-step devices and exploring the unique spherical torus (ST) parameter regimes to advance predictive capability. Non-inductive operation and current profile control in NSTX-U will be facilitated by co-axial helicity injection (CHI) as well as radio frequency (RF) and NB heating. CHI studies using NIMROD indicate that the reconnection process is consistent with the 2D Sweet-Parker theory. Full-wave AORSA simulations show that RF power losses in the scrape-off layer (SOL) increase significantly for both NSTX and NSTX-U when the launched waves propagate in the SOL. Toroidal Alfvén eigenmode avalanches and higher frequency Alfvén eigenmodes can affect NB-driven current through energy loss and redistribution of fast ions. The inclusion of rotation and kinetic resonances, which depend on collisionality, is necessary for predicting experimental stability thresholds of fast growing ideal wall and resistive wall modes. Neutral beams and neoclassical toroidal viscosity generated from applied 3D fields can be used as actuators to produce rotation profiles optimized for global stability. DEGAS-2 has been used to study the dependence of gas penetration on SOL temperatures and densities for the MGI system being implemented on the Upgrade for disruption mitigation. PMI studies have focused on the effect of ELMs and 3D fields on plasma detachment and heat flux handling. Simulations indicate that snowflake and impurity seeded radiative divertors are candidates for heat flux mitigation in NSTX-U. Studies of lithium evaporation on graphite surfaces indicate that lithium increases oxygen surface concentrations on graphite, and deuterium-oxygen affinity, which increases deuterium pumping and reduces recycling. In situ and test-stand experiments of lithiated graphite and molybdenum indicate temperature-enhanced sputtering, although that test-stand studies also show the potential for heat flux reduction through lithium vapour shielding. Non-linear gyro kinetic simulations have indicated that ion transport can be enhanced by a shear-flow instability, and that non-local effects are necessary to explain the observed rapid changes in plasma turbulence. Predictive simulations have shown agreement between a microtearing-based reduced transport model and the measured electron temperatures in a microtearing unstable regime. Two Alfvén eigenmode-driven fast ion transport models have been developed and successfully benchmarked against NSTX data. Upgrade construction is moving on schedule with initial physics research operation of NSTX-U planned for mid-2015.