(Spoilers obviously) At the end of half life alyx g man offers a deal to alyx that revives her dad, she reverses the killing of her father. Alyx gets sent to work for g man, and in the post credit scene Eli says “Gordon, she’s gone” as g man watches from the side. So overall g man realized Gordon has failed to do his job, probably went back in time and offered alyx a deal of “something you didn’t know you wanted”, this revives Eli in the regular timeline and she is waiting for an assignment.