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I'm looking for a story about a youthful (late teens?) female protagonist who begins the story by making an emergency escape from an orbital habitat. The protagonist is actually host to multiple disassociated (as many as seven?) identities, of whom she is initially unaware. They are capable of holding council internally, however.

Some of the identities/personalities are more sexual than others, leading to intercourse that only some of the personalities actively consented to.

Another spoiler-free notable story piece is a race of aliens who mark their 'naturally present' personalities/identities with a glyph or character on their bodies before venturing into public spaces.

FTL in this story must be performed by a non-human pilot, while the remainder of the occupants are either put to sleep or in suspended animation (I don't recall), due to eldritch somethings in the great beyond that will drive human pilots mad.

The driving action in the story is the protagonist's flight from corrupt human government groups that brutally experimented on her as a child to deliberately induce disassociated identities in an attempt to yield a viable human FTL pilot. The experiments were in fact successful, and the climactic scene involves the protagonist, now reconciled to her multiple personhood, piloting allies through an FTL jump.

I believe it was written in either in the late nineties or early aughts.

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You're describing This Alien Shore by C.S. Friedman:

This Alien Shore cover

Excellent book, I've reread it many times.

The protagonist

supports a dozen or more personalities, heavily augmented by implanted computers in her brain. She is unaware of this at the beginning of the book.

It's set in a universe full of Variants, mutated children of earth once cast off but now thriving. The various races were connected by the Guild, which has a monopoly on FTL travel - all others who attempt FTL travel fall victim to Sana, the dragons of the ainniq.

Guild members are almost uniformly of the Guerran race, which uses painted facial markings

to provide the social cues needed for wildly disparate personalities to work together harmoniously. The Guerrans essentially embody what we would call mental illness today, but taken to extremes and allowed to flourish for the gifts that come with those illnesses.

Many resent the Guild's monopoly, none more so than Earth, which has a genetic purity thing which is at odds with essentially the rest of the universe.

There's a major subplot involving hackers sleuthing to find the bad guy; ISTR that C.S. Friedman admits in the afterword to guessing and making up a lot of the technology, she actually captures many aspects of hacker culture, mindset, and motivation quite well.

Read the book, but... beware of dragons breathing red

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This Alien Shore by C. S. Friedman.From the book cover Earth's original superluminal drive did genetic damage to those who used it. Jamisia, protected by biological brainwave systems and accompanied by the many voices in her head. Shido is viciously attacked by coroporate raiders, Jamisia flees.When Outships can only be piloted by the Guera's Outspace Guild, whose abilities allow to monopolize galactic transportation

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