Question: In the year 2500, the main planets are all colonised for various reasons (Mars as another place to put the population, Mercury for minerals, etc.). The planet Mercury then becomes more and more rich, until its ruler declares himself emperor. 

In the year 2900, a war starts, lasting until 3000. At the end, people have been reduced to almost stone-age technology. My question is this: how would someone attack in a way that the people survive, while knowledge disappears.

Answer: 
Other Galaxies
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Probably not because unless there was a crazy breakthrough in technology that would allow us to explore all of the other galaxies in this universe. And plus we don't know if there are or aren't any other planets in our universe that are as technologically advanced like us. And the only way to remove all technology in the universe would be by somehow exploring every part of every galaxy in the universe, and removing all living species and removing all the technology that they have.

Constants
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Even if this were to happen we would be operating technology at the moment of trying to remove all technology, making it almost impossible to ever complete such a feat, and an exponentially less chance in 100 years.
There is a big technology monopoly. Everything is interconnected.

And then one of the parties released the computer virus. It took down all technology, power plants, hospitals.
Knowledge was gone, houshold appliances didn't work anymore, autonomous farming died out, people had no food.
No technology could function without the cloud. And the cloud was destroyed by the virus.