He died al kiddush Hashem. The Jewish community of York had gathered in Clifford’s Tower trying to protect themselves from a mob. The tower was surrounded, and the mob demanded that the Jews convert to Christianity, or they would be tortured to death. R’ Yom Tov paskened that the Jews should kill themselves rather than convert or go through the torture.
The men in the tower killed their families. R’ Yom Tov then killed the men, then killed himself. The few people who refused were eventually let out of the tower with promises that they would not be harmed, and would be allowed to convert. They were then killed.