It's a lasting trope of science fiction that when machines attain greater-than-human intelligence, humanity will be obsolete and machines will be hostile towards our existence. Some thoughtful authors have questioned this assumption. Notably (and outside of fiction) Kurzweil suggests that machine intelligence will be modeled on and an extension of biological human intelligence, and that there's therefore no fundamental incompatibility between the two.
It would be interesting to write a story from the perspective of benevolent non-biological humanity, directed towards hostile biological humanity. Imagine a situation where parts of the world advance to a primarily non-biological state and still view themselves as human. They may be regarded with suspicion and distrust by normal humans, if only because they are so far outside of normal human experience. I'm imagining a scenario where biological humans try to wage war against non-biological humans. But being of the benevolent sort, the non-biological humans don't want to do harm, and try to deflect and subvert the biological humans' anger and hostility without damaging either group.
With this background, there might be a short story with the following plot: A group of young men enter a transhuman city with the intent to destroy something important, driven by the ideology of their culture. They believe that transhumanity is evil, and they fully expect to die on their mission. However, they meet no resistance and are frustrated by the ineffectuality of their destruction and the lack of violent response to their actions. They meet other natural humans who try to talk with them, whom the crusaders regard with extreme hostility and suspicion. The crusaders believe the diplomats are some sort of trickery, "golems" in human form sent by the evil machines to deceive. In fact, the diplomats are the children of transhumans who have either opted to stay natural, or are waiting to become transhuman until they reach some level of development.
The diplomats urge the crusaders to stay (after they've exhausted their capacity for violence and are safe to approach), they show them the pleasures that their life in the transhuman cities afford, they attempt to teach them the truths of the high civilization. They waiver, and distrustfully allow themselves to be led deeper. Perhaps some are persuaded, but for the protagonist, it ends in tradgedy. He sees something that reactivates his hatred and fear, and he kills his guide (with whom there had been a love affair), only to find that she is indeed human. With her last breath she forgives him, and before she expires is rescued by her parents and brought into transcendence.
I'm imagining some striking imagery here, both of the horrible and the beautiful kind. His inner conflict grows and grows, and he witnesses her do some technological thing that seems magical. He remembers the biblical verse "thou shalt not suffer a witch to live," equates witches with machines, and seeks to dispel his inner conflict by proving that she is a machine. He snaps, takes his knife, and slashes her stomach open. To his horror, what spills out is not synthetic tubes and electronics, but blood and entrails. A machine swoops down on her dying body and treats it with tenderness that seems incongruous between metal and flesh. It lifts her gently into a gurney, settles her comfortably, staunches her bleeding, inserts IV's with care, brushes her hair from her face, grasps her hand, and flies away. Perhaps before it leaves, the machine turns on the protagonist with evident outrage and hostile intent, but is dissuaded from violence by some subtle, barely seen signal from the woman.
The machine will speak to him in a powerful, genderless, synthetic human voice. In will accuse him of killing its daughter, explain how its daughter had voluntarily sought to enlighten him, how she begged it to spare his life despite his horrible crime. "My daughter was good, and you have killed her. She's granted you a mercy that you don't deserve. You've killed her, but she will not die. I can save my child, but your child is already lost." (Implying that she had been pregnant, but neither had known it yet). It will be made clear somehow that the machine is being remotely operated by the parent, who is equally biological as the daughter but with synthetic enhancement.
The protagonist's revulsion shifts from the machines to himself. Maybe he tries to kill himself with the same knife, but as a compromise between its daughter's wishes and vengeance, the machine takes the knife from him and forbids him the release from remorse through death. He flees from the city and returns to his people. He's the only "survivor" of their little crusade, and he's too bitter to talk about the experience. He receives a mixed welcome; some think he was a coward and is ashamed of himself for not fighting, some attribute his recalcitrance to seeing horrible things in the city. He dies alone and misunderstood, thrown out of paradise by his own hand, and unable to be happy in normal life.