Galaxy proto-clusters at z >~ 2 provide a direct probe of the rapid mass assembly and galaxy growth of present day massive clusters. Because of the need of precise galaxy redshifts for density mapping and the prevalence of star formation before quenching, nearly all the proto-clusters known to date were confirmed by spectroscopy of galaxies with strong emission lines. Therefore, large emission-line galaxy surveys provide an efficient way to identify proto-clusters directly. Here we report the discovery of a large-scale structure at z = 2.44 in the HETDEX Pilot Survey. On a scale of a few tens of Mpc comoving, this structure shows a complex overdensity of Lya emitters (LAE), which coincides with broad-band selected galaxies in the COSMOS/UltraVISTA photometric and zCOSMOS spectroscopic catalogs, as well as overdensities of intergalactic gas revealed in the Lya absorption maps of Lee et al. (2014). We construct mock LAE catalogs to predict the cosmic evolution of this structure. We find that such an overdensity should have already broken away from the Hubble flow, and part of the structure will collapse to form a galaxy cluster with 10^14.5 +- 0.4 M_sun by z = 0. The structure contains a higher median stellar mass of broad-band selected galaxies, a boost of extended Lya nebulae, and a marginal excess of active galactic nuclei relative to the field, supporting a scenario of accelerated galaxy evolution in cluster progenitors. Based on the correlation between galaxy overdensity and the z = 0 descendant halo mass calibrated in the simulation, we predict that several hundred 1.9 < z < 3.5 proto-clusters with z = 0 mass of > 10^14.5 M_sun will be discovered in the 8.5 Gpc^3 of space surveyed by the Hobby Eberly Telescope Dark Energy Experiment.