Beyond the Light Horizon (Lightspeed Trilogy, #3) by Ken MacLeod

MacLeod's final book in the Lightspeed trilogy is nothing short of celestial.
  
The Fermi have departed from the rocky worlds, but they still haunt the gas giants. Their long-term intentions remain unknown. Hurled into the past by a time-slip, John Grant and his onboard AI navigate the long way back. They return to the present in a distant system, where they find Terre Nouveau, a human settlement already two hundred years old. Grant’s ship takes this astounding news to the far-roving Station, where Nayak has found new problems and a new lover. As the Station explores Terre Nouveau’s system, they encounter intelligent species far older than humanity, who are just as perplexed about the origins and intentions of the Fermi—a cosmic network of alien minds—as they are.

On Apis, rogue agent Marcus Owen rallies the native intelligent life against the human settlers, and passes on a warning from the Fermi: the humans must stop encroaching—or else. Myles and Marie take Owen’s warnings seriously. Other settlers are not convinced, and conflict erupts.

Owen is sent on a new mission, to Terre Nouveau’s colorful and verdant sister planet, where he finds that his arrival, and humanity’s, has been awaited longer than he expects.

As Earth’s empires—and other contenders—jostle for advantage around Terre Nouveau, John Grant works hard to expand his own business empire, in unexpected directions. But no one is prepared for how far the Fermi are willing to go—or for the unfolding of an audacious plan, millennia in the making, that reaches beyond the light horizon.