You're like marbles on glass

Plotwise, Alyx gets into Aperture Science by G-Man's will, and all she can remember clearly is Borealis. She gets to search for it, while some mysterious woman talks to her from observation rooms. She calls herself Aurora and claims that Alyx has better things to do than search for a ship. Too bad, mystery lady; Alyx wants her memories back and Borealis seems important. Also, Aurora turns out to be an artificial intelligence piloting a mannequin, so no reason to trust it, right?

Especially because she is a ship AI. Is she the Borealis itself?! It seems so for the longest time, until Alyx finds out there were two ships. Aperture purchased the Northern Star and the Northern Sea in the 1970s and tinkered with them ever since. One was named Borealis, the other one — Australis (two polar auroras). As every other big Aperture project ever, the ships eventually got their AIs/personality constructs, one male and one female, because of Portal thematic duality and stuff.

Borealis was rushed and disappeared inside a space-time anomaly created by its portal engine. Australis was never finished and was left to decay after GLaDOS killed everyone. Aurora is Australis (hence her eye glow when she is interfacing with her portal engine resembling southern lights). She pleads with Alyx not to follow her brother's path. Borealis became something different in the anomaly, something even she can barely recognize and for sure can't reason with.

So, Alyx has a choice to make: does she trust Aurora? Which Alyx is she, HLA one or EP2 one? She needs to collapse her own wave function to become one or another, to choose which reality becomes fully real.

Oh, and Borealis? Yeah, he is G-Man in this concept. G-man is Borealis’ personality construct. He is an Aperture creation like Wheatley or GLaDOS. He is a ship in human form, controlling space and time and teleporting wherever and whenever he wants. His employers are his former crew. He makes sure no one will ever find Aperture and create something like him ever again. Maybe he’s trying to organize his self-destruction. His eyes glow like aurora borealis. Also, his name is never mentioned in-text, just like it wasn't for Wheatley and GLaDOS.

Aurora is similar to G-Man but much less powerful (because the incident never made her this ultimate space-time bending entity). So, she is capable of blocking him on short distances in Aperture, navigating existing timelines and limited space-time manipulation, but not much more. Here’s my concept for her, based on the F-Stop stuff and 1970s nautical fashion.