On New Year's Eve1999 he gathered together the Torchwood 3 team to the Hub, except for Jack, and killed them all. Jack arrived later to find the carnage. Hopkins then shot himself. With everyone else now dead, Jack took over as leader of Torchwood 3. Hopkins had killed himself and the others as he saw the team unprepared for upcoming dangers in the 21st century and spoke of a storm coming which Humanity could not face. (TW: Fragments)
Per Torchwood policy, Hopkins' remains were presumably put into permanent storage in the Hub, although whether the morgue survive the destruction of the Hub during the 456 incident is unknown (TW: Children of Earth: Day One).
