A Deepness in the Sky (Zones of Thought series Book 2)

From inside cover Tor First Edition March 1999:

Thirty thousand years before the events of A Fire upon the Deep, Pham Nuwen is living in anonymity among the Qeng Ho interstellar trading fleet. In high orbit above the planet Arachna, they wait for the awakening of its dormant population, the Spiders, who have burrowed deep into the planet, awaiting the relighting of the On/Off star their planet orbits. For when light returns, Arachna will at long last explode into a Golden Age of technology and commerce.

But the slumbering Spiders' vulnerability has attracted another lurking presence -- the Emergents, a band of traders whose plans for Arachna are more sinister than anything the Qeng Ho could envision.

Reluctant to share their spoils with the Qeng Ho, the Emergents unleash an attack unlike any seen in the Qeng Ho's millennia-long history of exploration, reducing their fleet to serfdom... and then to something worse.

Reaching into memories so old and painful he can barely recall them, Pham gathers the other "survivors" about him and makes a final attempt to be worthy of a reputation as ancient and storied as the history of the Qeng Ho itself. But time is running out, for soon the Emergents' assault will strip Arachna bare.

As Pham's underground resistance cell struggles against its torturers in space, a wondrously gifted clan of Spiders on the planet below fights another battle - to advance their technology quickly enough to defeat their terrestrial foes, and to somehow overcome the invisible enemy lurking above.