When the player meets J. Katayama in Doom 3, he is in the thermal regulation pumps, hiding away from the demons. He questions why the player is there, stating that the player will make noise and attract the demons. He implores the player to leave, and tells him to take a keycard that will allow him to gain entry further into the Caverns. He then strongly affirms that he's not going to leave until he knows all the demons are dead. If the player persists in speaking to him, he will state that the player is making too much noise, and urge the player to leave and find help.
While his fate is ultimately unknown, he presumably perished along with the whole of Mars Base, as Resurrection of Evil states that the Marine was the only known survivor of Hell's invasion. However, there is a good chance he would have lived long enough to be rescued at the end of the game, assuming he did not leave his hiding spot.