Desmond Hart has a "great power," but where exactly did it come from? That was the single biggest mystery during Dune: Prophecy's first season. Turns out he didn't get it from surviving a sandworm attack on Arrakis. At least not primarily. The show's season one finale finally revealed how that soldier of the Imperium can murder people with his mind, but that answer raised an even bigger question. Someone -- or something -- used thinking machines to implant computer technology inside him. That forbidden machinery allows Desmond Hart to activate a bioengineered virus that could destroy mankind.
We don't know if Shai-Hulud actually consumed Desmond Hart or not. It seemed as though it had, but after "The High-Handed Enemy" it's not clear what actually happened to him that fateful day on Arrakis. We do know what happened after Hart survived his encounter with that sandworm. Someone chose him to become an unwitting tool of thinking machines and their possible human allies. (The fact Hart came in close contact with Shai-Hulud, and therefore might have had some natural abilities greattly enhanced via spice, could be why they used him as a weapon.)
After the sandworm left Desmond behind an unknown figure used thinking machines to remove Hart's eye from his skull without detaching it. They then placed nanotech on his optic nerve. While we don't know exactly how Hart can activate that machinery, we know what it does. Hart uses it to activate a bioengineered virus lying in wait in the amygdala of people who don't even know they're infected. They carry a new, modified version of the Omnius Scourge, a fatal virus that the thinking machines and a human ally used against humanity. The original version attacked livers, as Mother Raquella (via Lila) explained in episode five.
This terrifying variation's place on the amygdala literally turns fear into a mind killer. The series didn't confirm how the virus spreads, but Hart seems to be patient zero who is not only activating it but infecting others with it. Him also being sick as his mother Tula said would explain why his own back burns and scars. It would also explain how the virus made its way to Wallach IX and the Sisterhood, who then all had the same visions of the "eyes" from Desmond's procedure. He came in contact with Kasha on Selusa Secundus when he first arrived at the palace.
The more fear someone feels the more the virus burns them from the inside out. That's how Desmond Hart killed his victims. He doesn't have super human abilities. The thinking machines advanced nanotech activates the virus while making it seem as though its entirely Hart's doing.
Even with their training neither Reverend Mother Kasha nor Sister Nazir could fight the infection. Nazir knew specifically what she needed to do and still succumbed to the dangerous virus. It was only when Tula guided her sister Valya that any member of the Sisterhood learned how to defeat the virus. Valya had to let the fear wash over her rather than actually feel it.
But just because the highly-trained Valya was able to do that doesn't mean humanity is not in existential danger from this virus. Especially when not even the Reverend Mother Superior knows who is responsible for making and spreading it. She could not see who owned and operated the thinking machines that put the nanotech in Desmond.
Could it be a thinking machines that survived the great war without humans knowing? What about the the Ixians, the faction of humans who deal in illicit technology that Keiran Atreides bought from during season one?
Or could it be a member of the same humans who helped the robots make the original version of Omnius Scourge? It's a notorious group Dune: Prophecy mentioned by name in its season one finale, the Tlulaxa. One of their genetic scientist helped a robot make the first version of the virus used against humanity before. The Tlulaxa is also the same group who made Sister Theodosia into a shape-shifting Face Dancer.
Someone, something, or human and machine working together used forbidden technology to turn a soldier into a weapon. They then unleashed both him and a deadly fear virus on the Sisterhood, the Landsraad, and all of humanity. We just don't know who, or maybe what, they are. That's a much bigger question than how Desmond Hart got his "great power" in the first place. And it's one only Valya Harkonnen might be able to answer.
Editor's Note: Dune: Prophecy is a Legendary Entertainment production. Nerdist is a subsidiary of Legendary Digital Networks.