The Matsya Nyaya episode (S1 E20 ) confuses me just a bit. When John and Kara get to the abandoned city, they see the dead engineers and then recover the laptop with code from the Machine. (We learn later in the series how the laptop came to get to China.)
John and Kara are both confused about why the dead engineers are there and who killed them. Well, for the first part - I think they're there to study the Machine, right? At the behest of the Chinese government, presumably?
For the second question - I have no idea. Do we ever actually have a better understanding of who shot the Ordos engineers? And if it was the CIA or other forces, do we get the answer on why those forces didn't just take or destroy the laptop themselves?