On New Year's Eve1999, Alex gathered the Torchwood Three team in the Hub, except for Jack, and killed them. Jack arrived to find the carnage. Hopkins then shot himself. With everyone else now dead, Jack took over as leader of Torchwood Three. Hopkins had killed himself and the others as he saw the team unprepared for upcoming dangers in the 21st century. He spoke of a storm coming which humanity could not face (likely the Miracle Day). (TV: Fragments)
Under Torchwood policy, Hopkins' remains were presumably put into permanent storage in the Hub, although whether the morgue survived the destruction of the Hub during the 456 incident is unknown. (TV: Children of Earth: Day One)
