Nanovirus uplifts spiders instead of monkeys
Terraformer Avrana Kern seeds a green planet with monkeys and an uplift nanovirus, but an insurrection destroys the monkey payload and the virus instead infects Portia jumping spiders, whose civilisation then evolves over thousands of years under the distant watch of Kern, uploaded into a satellite. Meanwhile the last humans, on the ark ship Gilgamesh, arrive to claim the planet and fall into mutiny, cult and war, while the spiders progress. The ending turns on the spiders rewriting the virus to give the humans empathy, so the two species can coexist rather than one exterminating the other.
