Really nice conituation.  Good work developing the different species. 

I liked how Shia's response was "I'm the ship." 

You are doing well to make Shia into a benign manipulator.  She is constantly pushing her companion to grow and become stronger.

The discussion about passing judgement and who should die was a good one.  I recall in one Doctor Who episode, he was on a space cruiser called the Titanic, filled with lots of rich people on a tour.  Well, the former owner of the company who does the cruises and ships was booted out and planned on destroying the ship and having it crash on Earth.  The reason is to cause enough of a scandal to throw his mutinous board, who voted him out of office, into jail.  The Doctor, without his TARDIS, had to work to save as many as he could but among his group of a good, strong willed woman, old man, a poor couple who worked hard and won tickets in a contest to go on the cruise, a heroic cyborg who sacrificed himself to take out some of the killer robots, and a cowardly rich arrogant jerk whose first thoughts after the the Doctor saved the day was how he sold the his shares in his the bad guy's company to his rivals, making him even richer.  Of them only the old man and rich jerk survived.  The old man noted to the Doctor if he could have decided who to should survive and who not, the rich man wouldn't be a survivor but at the same time doing so would make the Doctor a monster.

I liked how Shia noted she wouldn't feel shame in not helping people.  If there was an alien Hitler trying to escape on a damaged ship about to explode, such a man would likely be left to die.  Or, saved but disabled so those he wronged could bring justice onto him.

I liked how Shia was so honest about their plans to save and protect humanity from itself and others happening frequently.

Considering in the previous section, I asked how she would feel if she was willing to let her core suffer damage rather than hurt Brian, I imagine that would be a huge debate among her kind.  Some could even see Brian as a virus to the system that needs to be purged. 

It was also funny how their "strong" encryptions were useless to Shia.  I imagine tapping into Brian's memories and any knowledge he might have on the better ones helped her out, if she needed any at all.

It was also interesting to hear her comment she is still talking with other people.  Might she consider picking another person up in another section of herself?  Or only if it was to save the person's life, like if they were in a life pod from an exploded ship. 

She could end up being the only girl in your collection where a harem is very much possible.  But the harem guys wouldn't know it at all.

Really, a great piece of work.