|“||Daniel was my son. My wife, God rest her, she didn't die natural. Daniel and I buried her together. After... well, hunting, that's, that's what got us through. Then the angel war started. I had been called up to serve before so they gave me a platoon I guess you could call it. Dan was in it. We got separated. I guess you can figure where this is headed. (...) I'm the one who brought him to war. I'm the one who sent him to die. I don't even know what they did to him. The angels took him. We never found the bodies. I never figured I'd be any kind of a father to a child. But Daniel... was the best thing in my life.||”|
When the Apocalypse began, Bobby was assigned to command a platoon of which Daniel was a part. Daniel eventually got separated from his father and killed by the angels. Bobby never discovered how his son died as the angels took Daniel and the other members of the platoon they killed and their bodies were never found. After Daniel's death, Bobby believed the war would kill him too and after traveling to the Main Universe, began trying to kill himself through hunting.
In 2018, Bobby encountered a manifestation of his fears regarding Daniel's fate, conjured by the enhanced djinn Neil. The manifestation of Daniel had burned out eyes, similar to a victim of an angel smiting and brutally beat his father before shoving him up against a tree and stabbing him through the shoulder with an angel blade. Daniel claimed that the angels had crucified him "piece by piece" and went to stab Bobby with another angel blade before they were interrupted by Mary Winchester.
Daniel advanced on Mary who shot him several times to no effect. Daniel tackled Mary to the ground and began strangling her to death. Distressed, Bobby removed the angel blade from his shoulder, tackled Daniel to the ground and apologized to his son before stabbing the manifestation through the heart with the angel blade, causing it to explode into dust.
Later, after the hunt, Bobby explained to Mary what had happened to his son while she treated his injuries.
Sometime later, when Dean visited Mary at Donna Hanscum's cabin, Mary tells him that Bobby is out at the moment and that they had needed some time apart after what had happened with Daniel.
- The existence of Daniel in Apocalypse World is a major deviation from the Main Universe Bobby's life as he had refused to have children with his wife before her death. This Bobby told Mary that he never thought he would be much of a father, but Daniel was the best thing in his life.
- In Bobby Singer's Guide to Hunting, Sam speculates that Karen was pregnant at the time of her death which was the memory Bobby held dearest and Oblivion wanted. However, the book is non-canon and contradicted by later events in the series, particularly the events of Death's Door.