The structure and evolution of the universe at large scales is dominated by dark matter, particularly large clumps of dark matter called “dark matter halos.” Soon after running the first large scale, high-resolution simulations, researchers realized that the growth of these dark matter halos was closely tied to their surrounding environment. This connection is called “assembly bias.” Although this behavior is well-understood for the largest halos, the cause of assembly bias for smaller dark matter halos (such as the one which contains our galaxy, the Milky Way) has remained a mystery for the past fifteen years. This thesis aims to resolve this mystery through a synthesis of previous approaches. Accomplishing this goal requires constructing a substantial theoretical framework. One of the leading proposed causes for assembly bias stems from ambiguity of where halos end and where their surrounding environment begins. To this end, I develop Shellfish, the first code which is capable of measuring the boundary between the two, the “splashback surface.” Additionally, the study of assembly bias requires detailed analysis of large “cosmological” dark matter simulations. However, despite the long tenure of these simulations, there remain main unanswered questions about their accuracy. I perform extensive tests on the reliability of cosmological simulations, assessing the reliability of every major property of dark matter halos, and identifying previously unknown numerical biases which significantly impact a number of widely-used simulations. Finally, using Shellfish to identity halo boundaries and these numerical tests to ensure reliability, I tackle the problem of galaxy-mass assembly bias. I identify the exact halos which are responsible for the assembly bias signal and use this identification to isolate the processes which lead to assembly bias. This analysis shows that galaxy-mass assembly bias is primarily caused by misidentified “splashback” subhalos, although a modest fraction of the effect comes from a small number of halos in massive filaments whose growth is slightly slowed by the tidal fields of their filaments and by gravitational heating.