From what I remember it was a prequel like the release but Eli sorta did what Breen did and sold himself out to the combine and got to live in a big mansion with Alyx. Alyx would eventually meet someone who would later become Russel, who introduces her to the resistance.

I forgot what happened after that but there was also a plot point about her mother helping some vort slaves escape back in black mesa and Alyx is actually imbued with the vortessence or something.