Shadow Captain takes place in a setting 10 million years in the future called The Congregation, where the Solar system has been through thirteen "Occupations" that has reduced the planets to rubble and rebuilt it into its current state, a collection of 50 million micro-worlds, with 20,000 of them occupied by the remnants of humanity and alien species.

The crew meets with Mister Glimmery who is infected with the "glowy" like Fura, in his presence is an alien Crawly named Cuttle.

Eddralder leaves six syringes with an antidote, and joins the crew of the Revenger with Merrix, promising to radio back how to cure the poison.

As the trams near the central chamber the quoins begin glowing bright white and emit a scream that's heard inside their heads.

Returning to Revenger they discover the same is true throughout the 20,000 worlds, and fear that this financial event may cause the end of the Thirteenth Occupation.

Their plan at the end is to go into hiding by pursuing the object that Adrana believes is orbiting the Old Sun at intervals coinciding with Shadow Occupations.

Paul Di Filippo at Locus Online gives a generally favorable review of Shadow Captain, saying: "what Reynolds is really doing is channeling some of the great writers from what David Pringle calls the Age of Storytellers–Dickens, Stevenson, Sabatini, Dumas–into space opera form [...] This second installment is a highly entertaining and worthy successor to Revenger.