Karn had left Konoha because a Bounty Hunter at the Underground Bounty Station had found information on Shennong.
The man kept quite a high profile. Perhaps he had never expected someone like Karn to set his sights on him, so he had barely bothered concealing his identity. Word of "Doctor Shennong" had already spread through several small countries, and he had even visited some towns and villages in the Five Great Nations.
With ten million ryō on offer, Shennong's whereabouts were soon pinned down. The people tracking him specialized in gathering information for the Underground Bounty Station, and Shennong had not noticed them at all.
By the time Karn arrived in the Land of Demons, Shennong was still treating people's injuries in a village there.
After sending the Bounty Hunter away, Karn went in alone.
With his heart full of a thirst for power and hatred, Shennong still traveled around the Shinobi World treating people. Karn did not believe he was that kindhearted. Most likely, he was pursuing his own goals while treating others.
Researching forbidden techniques, for instance, required plenty of test subjects. But he could not expose his identity and bring Konoha's pursuers down on him, and he had no powerful organization behind him, so he could only conduct his research slowly this way.
Karn found that explanation more believable than the idea that Shennong simply wanted to treat patients.
After entering the village, Karn found Shennong treating the villagers with Medical Ninjutsu. He seemed so absorbed in his work that he did not notice Karn approaching from behind.
"Imperius Curse!"
Once Shennong finished treating the villager in front of him, Karn suddenly attacked him with the Imperius Curse. He did feel some resistance at first, but against Karn's immense magic, Shennong's resistance was utterly insignificant.
"Doctor Shennong?"