hmm... not good...

I feel like some people aren't familiar enough with the original game that they miss the significance of Alex trying to enter the teleporter in Bubby's lab before Gordon. Because in the original game, that's how it's meant to go - Alyx goes in the teleporter and is successfully sent to black mesa east to reunite with her father, Eli, then Gordon goes in. Alex was just following her programming - playing the role she was made for. But Eli doesn't exist anymore. He has been replaced by an imposter wearing her father's face. Kleiner and Barney have also been replaced and aren't there to look out for her anymore. She's alone, just trying to follow the only path she knows, in a world where that path no longer exists and is actively being overwritten by new ones.

that... that Woman. is waiting for us, crosslegged, on the Floor. That, is what people in San Francisco do and that's where all the Scientists™ Are From.