For more info on B.J.'s backstory, see this page.
Weeks after the events at Isenstadt, B.J. is ordered by the OSA to stop Deathshead's plans to find the Dark Relic. He traverses through a village and the sewers before reaching the crypt where the Dark Relic is located. However, he is captured and had his face damaged by Karl Von Starke, one of Deathshead's assistants and locked in a cell.
However, B.J. escaped his cell and went to stop Deathshead from unleashing the Dark Army. On the way, B.J. encounters Karl's brother, Wilhelm Von Starke. After an intense gunfight, Wilhelm is killed, allowing B.J. to continue to Deathshead. When he finally confronts him, Deathshead unleases one of his soldiers powered by the Dark Relic, but B.J. defeats it after a long gunbattle. However, Deathshead has went further into the base and seemed to have set off an alarm.
Just then, B.J. recieves a call from Jack telling him that a mercenary group infiltrated the base and warns him to escape.
B.J. is apparently captured by Deathshead and locked for weeks until he forces him to help him defeat Karl.
B.J.'s story continues in Wollfenstein: The Old Blood.