A well written story with a lot of character to the lore. As mentioned by Hobby Fuzion, it definitely reminded me of 2001, ("I'm afraid I can't let you do that"). I had the same thoughts on what the adversary was as well. Machine Cult Defilers and Robot Legions crossed my minds, as well as some bizarre sort of demonic faction. Captain Maya Tem is extremely well developed for 1000 words.
Curious on your thoughts of what was the unconventional weapon here? The boarders and their mercurial forms? The ship's AI, which prevents the captain from completing her action at a pivotal moment? The Gravsuit for being the thing that truly stops her?