Years ago I bought a new Sci-Fi book. Likely published between 1998-2006. It stood out to me because I think it had won some sort of award and it was featured in a bookstore that did not predominatantly sell Sci-Fi.
The size of the book was larger than the typical soft cover printing and there was a design some of some darkened space scene on the front (I know, I know, not helpful)
The Plot: I have forgotten the main part of the action/adventure. But what struck me was the fact that the main character (female) was trying to figure out who her true enemies were throughout most of the book. At times this included her non-corporeal A.I. (her spaceship?) that had been with her most of her life.
The enemies are vanquished in the end. And as all things are revealed, it turns out to be a beautiful love story between the woman and the A.I. One that is not bound by conventions of gender or form. I believe that they are able to share their consciousness directly with each other somehow.
The description of this melding of souls was something that haunted me over the years and regret immediately giving the book away to a friend. I have even had a few dreams about it... which I hope has not further muddled my memory of the story.
It was suggested to me that it might be Ancillary Justice, but the plot and the publishing date aren't quite right. Still, it is next on my list to read, I hear it is good.