The ending and "new" ending, so that you don't have to play this. It looks like the idea is to force the plot of the second game and third, which made ZERO sense in comparison to the first one due the change of writers and how the mysterious aliens from the first game went from being mysterious and neutral... To LOOLEVIL!!!
Iirc, in the first game the marker is some alien device of unknown purpose, which repurposes all biological matter in its vicinity as a defense mechanism.
In the second, the protagonist is revealed to have gone insane and is building copies of it for unknown reasons (and the government is helping him, for even more unknown of a reason, probably something something bioweapon research). I think you also have a direct conversation with the new marker, but I can't recall what it says.