Longer summary of Harmonies of the Net, as preceded by Groundties and Uplink.
The trilogy tells one convoluted, complex story, starting with the discovery by Power That Be that the interstellar civilization's datanet, its unifying channel for communcation and information of all kinds, appears to be eroding in some unexplained way. This is, by current theory, impossible.
A student's doctoral thesis at the prestigious Vandereaux Academy suggests a possible cause for the problem in an obscure paper published (and ignored) some years earlier. The student, Steven Ridenour, is rushed through graduation and onto a transport which will take him to meet with the author of the first paper, J. Wesley Smith, in the hope that their combined talents will come up with a solution to the 'net problem now threatening life as this galaxy knows it.
The brand new Dr. Ridenour, a barely-twenty whiz-kid with far too much academy polish to be natural, impresses the senior crew of the transport ship, including Admiral Loren Cantrell, an experienced trouble-shooter for the governing Council. She has spent her career dealing with the problems arising from a society that considers itself primarily based on space stations, with colonized planets left in a second-class position, stigmatized as "Recon" or Reconstructionists of earlier ethnic cultures. This is a political stance the admiral finds dubious, but it carries great weight in the Council.
J. Wesley Smith, after his unsuccessful early paper, has been shuffled into a research community on the planet HuteNamid, whose colonists recreate Native American culture on their richly beautiful world, emphasizing the essential beliefs of unity with nature. He (and many of the other researchers assigned there) are happy within the HuteNamid community and not anxious to leave.
It quickly becomes clear that the disruption of the datanet does, somehow, originate at HuteNamid, and Admiral Cantrell takes drastic measures to isolate the HuteNamid system from the rest of the datanet while Ridenourand Smith -- and anyone else who seems to be involved -- are to investigate and correct it. Steven Ridenour, a product of the most intensely elite and space-based institution in the galaxy, barely tolerates landing on the planet, becoming physically ill. He impresses the researchers and natives as a posturing prig, not that they'd expected anythingelse. Before he can find his balance, he runs afoul of one HuteNamid faction that believes he and the datanet research team will disrupt the planet's gods with their meddling.
He is rescued barely in the nick of time from near-death by his local guide, Anevai Tyeewapi, who is horrified by her cousin Nayati's violence toward Steven. Nayati disappears and Steven is put back together and heals, not without opening up some unpleasant old memories of being persecuted by other academy students. During the investigation that follows Steven'smemories of a planet-based childhood come to the fore; as an ex-Recon himself, he has spent his life proving himself past reason, sanity and health to everyone at Vandereaux. His expertise on the 'net has already proved him to both Smith and Cantrell's own 'net expert, but Steven's paranoia is not easily turned off.
The datanet investigation by Smith and a somewhat-recovered Ridenour proceeds on HuteNamid, discovering one reason that the HuteNamid authorities have been very reluctant to cooperate. It also provides a seeming link with an old mystery from Cantrell's early career, of another planet where the Recon settlers destroyed themselves and also the planet's biosphere. Preventing such a disaster on HuteNamid becomes a second urgent reason for the investigation. Smith and Ridenour speak the same technical language, but each makes assumptions about the other that lead to extreme miscommunications. Less miscommunication takes place between Steven and Anevai, she seeing through the Vandereaux polish more quickly than those, like Smith, who come from that society and take it seriously.
The central authorities at Vandereaux, disquieted by Cantrell's action of cutting HuteNamid even temporarily out of the universal datanet, and increasingly disturbed by the datanet's instability, send two more agents to oversee Ridenour's progress. These are pure Council-agenda politicians, and their pressure tactics revive more of Steven's hellish past memories. He has learned, barely, that such a thing as honest friendship might exist with Wesley Smith, and turns to Smith before he leaves for some reassurance of his own worth -- with disastrous results.
One more attempt to find the source of the 'net disruption leaves the situation resolved, in a way, in a final turnaround.