Beyond the Dragon’s Gate by Yoon Ha Lee

Beyond the Dragon’s Gate by Yoon Ha Lee (Tor.com, 20th May 2020) opens with Anna, an ex-academic who used to work in AI research, arriving at an orbital fortress after being abducted by the military. After seeing the wreckage of several spaceships she learns from the Marshal commanding the military that the AIs that control these vessels have been committing suicide. He then tells her that he wants her to communicate with them mind to mind to find out why (even though her academic partner Rabia died from this process during their research).
When the Marshall takes her to see one of the surviving ships, Proteus Three, Anna sees how radical the previously discussed modifications have been:

They’d emerged above what Anna presumed was a ship’s berth, except for its contents. Far below them, separated from them by a transparent wall, the deck revealed nothing more threatening—if you didn’t know better—than an enormous lake of syrupy substance with a subdued rainbow sheen. Anna gripped the railing and pressed her face against the wall, fascinated, thinking of black water and waves and fish swarming in the abyssal deep.
[. . .]
“You’re going to have to give me an access port,” Anna said after she’d taken two deep breaths. She stared at the beautiful dark lake as though it could anesthetize her misgivings. “Does it—does it have some kind of standard connection protocol?”
The Marshal pulled out a miniature slate and handed it over.
Whatever senses the ship/lake had, it reacted. A shape dripped upwards from the liquid, like a nereid coalescing out of waves and foam, shed scales and driftwood dreams. Anna was agape in wonder as the ship took on a shape of jagged angles and ragged curves. It coalesced, melted, reconstituted itself, ever-changing.
“Talk to it,” the Marshal said. “Talk to it before it, too, destroys itself.”

The story ends (spoiler) with Anna communicating with the ship until she starts having convulsions. The Marshal breaks the link and then, after Anna recovers, she tells him the modifications that they have made to the spaceships have left the AIs with suicidal levels of dysphoria.
This story has a colourful setting and some interesting detail (the background war, the fish-dragon pets, the orbital fortresses, etc.), and the amorphous, water-like spaceships are intriguingly strange—but the resolution is too abrupt, and leaves the story feeling like an extract from a longer work. I’d also add that the reason for the AIs’ suicides reduces what is here to a simplistic trans message.
** (Average). 3,900 words. Story link.