Shortly after the Deep Space Nine series finale, Dr. Julian Bashir is once again confronted by Section 31. The group is Starfleet's 'black ops', answerable to no one. They convince Bashir to go take on Locken, a man who had taken over an enemy facility and wishes to restart a new race of genetically enhanced super-beings. Both Bashir and Locken themselves are genetically enhanced.
In Voyages of Imagination, the plot for the novel was originally developed shortly after Star Trek: Deep Space Nine ended. Pocket Books editor Marco Palmieri recalled, "One of the great things about David's involvement in the project was that Abyss was the story that followed up on Avatar. It was extraordinarily cool to have one of DS9's TV writers developing a story for the post-TV fiction, with its mix of old and new characters."
On the subject of collaborating with David Weddle, Jeffrey Lang remarked, "My contribution to the story were plot details and the character bits. In particular, I'm pleased with the characterization of Taran'atar. He was pretty much a tabula rasa when I got him and it was fun to try to figure out what made him tick. Also, I tried to make Locken the Pseudo-Khan less of a 'Bwah-ha-ha' villain and more of a tortured soul."