Now that that is out of the way, i will explain a bit more about the new version.
During the Combine's occupation of earth, Gordon is taken from stasis and taken with Eli, Kleiner and Alyx to Black Mesa. However, Gordon must fight through the ruins of the previous City 17 before he can complete his task, to destroy Project Sigma, a machine to harness the power of Xen Crystals to open interdimensional portals, not only limited to Xen, which the Combine intend to use to create superportals and invade other galaxies.
Some may say 'BLACK MESA WAS DESTROYYYYED' which was only true in the expansion packs such as Blue Shift or Opposing Force, which could be considered alternate realities.