Former Half-Life franchise scriptwriter Marc Laidlaw has published what appears to be part of the Half-Life 2: Episode 3 plot on his personal website. Laidlaw left Valve over a year ago.
The text that was published on Laidlaw's personal website appears to be a modified version of a part of the original Half-Life 2: Episode 3 plot. Important names, genders, races and events have been slightly altered, likely to avoid legal issues.
In the published plot players can read that Gordon Freeman and Alyx Vance do indeed make their way to the Borealis in Episode 3 and that they set out to destroy the ship just as requested by Alyx's father Eli, despite requests from Dr. Mossman to return the ship's technology to the resistance.