The art of cosmography, i.e. map-making of the Universe, is essential for the progress in astronomy. In this talk, I present a new technique to reconstruct a large-scale structure of the intergalactic medium (IGM) using a unique combination of the narrow-band filters with Subaru/HSC. The technique is applicable to high redshifts across z~4-6 and is perfectly suited to examine the ionizing radiation and the gaseous environment of galaxies and quasars. I demonstrate the method using the public release of HSC data and present the first co-spatial, large-scale map of the Lyman-alpha emitters and the IGM in the COSMOS field at z~5. I also discuss the potential applications of IGM tomography and the implications for our understanding of reionization and the growth of supermassive black holes.