To study the atomic, molecular and ionized emission of Giant Molecular Clouds (GMCs), we have initiated a Large Program with the VLA: 'THOR - The HI, OH, Recombination Line survey of the Milky Way'. We map the 21cm HI line, 4 OH lines, 19 H_alpha recombination lines and the continuum from 1 to 2 GHz of a significant fraction of the Milky Way (l=15-67deg, |b|<1deg) at ~20" resolution. In this paper, we focus on the HI emission from the W43 star-formation complex. Classically, the HI 21cm line is treated as optically thin with column densities calculated under this assumption. This might give reasonable results for regions of low-mass star-formation, however, it is not sufficient to describe GMCs. We analyzed strong continuum sources to measure the optical depth, and thus correct the HI 21cm emission for optical depth effects and weak diffuse continuum emission. Hence, we are able to measure the HI mass of W43 more accurately and our analysis reveals a lower limit of M=6.6x10^6 M_sun, which is a factor of 2.4 larger than the mass estimated with the assumption of optically thin emission. The HI column densities are as high as N(HI)~150 M_sun/pc^2 ~ 1.9x10^22 cm^-2, which is an order of magnitude higher than for low mass star formation regions. This result challenges theoretical models that predict a threshold for the HI column density of ~10 M_sun/pc^2, at which the formation of molecular hydrogen should set in. By assuming an elliptical layered structure for W43, we estimate the particle density profiles. While at the cloud edge atomic and molecular hydrogen are well mixed, the center of the cloud is strongly dominated by molecular hydrogen. We do not identify a sharp transition between hydrogen in atomic and molecular form. Our results are an important characterization of the atomic to molecular hydrogen transition in an extreme environment and challenges current theoretical models.

THOR: The H i, OH, Recombination line survey of the Milky Way