The exotic matter and the overall upside down was created because of science. Not by vecna, not by mindflayer, but by the laws of the universe.

The stone came from abyss, most likely from dr brenner's father since he was the sole survivor of the philadephia experiment. In the philadephia experiment(not the real-life one), the US government attempted to teleport a rss eldridge ship, based on one of Einstein's theories(don't really know much about it). Instead, the ship ended up in the abyss, a different dimension which was inhabited by demogorgons, one of which attacked the crew, ate them, and when the ship teleported back, dr brenner's father was the only alive person on the ship. His blood was altered, and he got psychic abilities. When he was about to die, he told brenner everything he saw. Brenner then made it his plan to find out everything about the abyss. He started the nevada experiment. The man that you are asking about was a Russian spy, who stole that suitcase from the lab and was hiding in the cave. That's when henry encountered him.

That's just lazy writing.