Recent Lyman-α forest tomography measurements of the intergalactic medium (IGM) have revealed a wealth of cosmic structures at high redshift (z ∼ 2.5), including detection of large voids and protoclusters. In this talk, I will present the Tomographic Absorption Reconstruction and Density Inference Scheme (TARDIS), a new chrono-cosmographic analysis tool for understanding the formation and evolution of these observed structures. We use maximum likelihood techniques with a fast non-linear gravitational model to reconstruct the initial density field of the observed regions. This allows us to not only accurately reconstruct the cosmic web at z~2.5 from the observed Lyman-alpha forest, but also to track the trajectories of coeval z = 2.5 galaxies to their z = 0 cosmic web environments and shed new insight in galaxy formation and evolution.