Nanocrystalline metals have been a topic of great discussion over recent years due to their exceptional strengths and novel grain boundary-mediated deformation mechanisms. Their microstructures are known to evolve through dynamic processes such as grain boundary migration and grain rotation, but how the collective interaction of these mechanisms alter the microstructure on a larger scale is not completely understood. In this thesis, we present coupled atomistic modeling and experimental tasks that aim to understand how the grain structure, grain boundaries, and associated grain boundary network change during nanocrystalline plasticity. Due to the complex three-dimensional nature of these mechanisms and the limited spatial and temporal resolution of current in-situ experimental techniques, we turn to atomistic modeling to help understand the dynamics by which these mechanisms unfold. In order to provide a quantitative analysis of this behavior, we develop a tool which fully characterizes nanocrystalline microstructures in atomistic models and subsequently tracks their evolution during molecular dynamics simulations. We then use this algorithm to quantitatively track grain structure and boundary network evolution in plastically deformed nanocrystalline Al, finding that higher testing temperature and smaller average grain size results in increased evolution of grain structure with evidence of larger scale changes to the grain boundary network also taking place. This prompts us to extend our analysis technique to include full characterization of grain boundary networks and rigorous topographical feature identification. We then employ this tool on simulations of Al subject to monotonic tension, cycling loading, and simple annealing, and find that each case results in different evolution of the grain boundary network. Finally, our computational work is complemented synergistically by experimental analyses which track surface microstructure evolution during sliding wear of nanocrystalline Ni-W thin films. These experiments track the development of a surface grain growth layer which evolves through grain boundary mediated plasticity and we are able to make direct connections between this evolution and that which was observed in our simulation work. All of the findings of this thesis are a direct result of the dynamic and collective nature by which nanocrystalline materials deform.