Johann Weyer is a former pupil of Agrippa. He turned out exceptional and outgrew Agrippa in many ways, becoming more powerful than his mentor. From what is said in-game by Agrippa himself and in his letter to Weyer, it seems that they are very loyal to each other. Agrippa was helping his student in his research of Orbs, describing what happened when he had found one of them and Johann once tried to free Agrippa from Alexander's imprisonment. He failed because of Agrippa's uncertainty. He refused to try again, because Alexander might have captured him too.
From what little is known about him in-game, it appears that Weyer was able to unlock the powers of the Orbs, and left this world. Weyer had managed to assemble an entire collection of orbs and separate the living nightmare, that is the Shadow, from them. Alexander asked him to help him escape as well, but Johann refused, demanding that he free Agrippa first. He gave Alexander a recipe for a tonic that would allow Agrippa to be released from the dead husk he'd been imprisoned in without killing him.
In the end, it turned out Alexander was unwilling to use the potion because he wasn't sure if Weyer would take him to his world along with Agrippa. From that point, Daniel became the last light of hope for both Weyer and Agrippa to get out of this situation.
If Daniel chooses to put Agrippa's head in Alexander's portal, the game ends with Daniel walking towards a group of hovering blue lights while Agrippa appears to be talking to Johann and assuring Daniel that he'll be safe.
This is almost certainly an allusion to Johann Weyer (1515-1588), who was a Dutch doctor and an important figure during the witch hunting era. He was a follower of Heinrich Cornelius Agrippa, also alluded as a character in the game.
Both the real Johann Weyer and Agrippa lived in the 16th century, while the game is set in the 19th century. This suggests that they must have prolonged their lives using similiar methods to those used by Alexander.