Jonathan Ishii was a scientist who was part of the Delta Science Team. He disappears shortly before the demon invasion. The player's first assignment in Doom 3 is to find Ishii. Sergeant Kelly dispatches the player, following reports that Ishii was spotted in the Mars City Underground approaching the airlock that leads to the old communications array. Kelly instructs the player to bring Ishii back unharmed.
When the Player finds Ishii, the scientist panics and begs the Player to let him send a transmission to Earth warning them of Dr. Betruger's experiments. Ishii cryptically adds, "The Devil is real...I know, I built his cage."
Suddenly, the main portal in Delta Labs activates and demonic spirits come pouring out. Ishii is possessed by one of these demon spirits (as are many other humans throughout the base) and he becomes a zombie as a result. Ishii is the first enemy the player faces in the game.
- It is possible to kill Ishii before he is possessed.
- According to the Making of Doom III book, the original story had Ishii commit suicide by shooting himself in the head rather than become a zombie.