That depends on what adaptation you've been watching.
Didn't the Dark Man turn out to be Gordon Freeman with the Combines' science and outer space?.
Inspired by his progress, he decides to give his life to ensure humenkind's victory after failing to be of any service to mankind as well as his brother. John Freeman gives chase and sees Henry Freeman waging war on the Combines. On top of this, the Combines are apparently led by the Dark Man, who is implicitly not humen by virtue of his title as a "man" (he only looks like humen and Combine perhaps he is some kind of amalgam powered by "science"?). The Combines, knowing of the events in John Freeman's world, use portals to take Gordon Freeman's zombified body and not only bring it back to life, but conscript him with the "science" implants. Henry Freeman's side of the family lives in a civilization of very similar beings to themselves. The apparent misspelling of the word "human" is consistent throughout the Hero Beggining arc and doesn't happen in any other squirrelking stories.