After arriving, John saw his by then elderly son Alan, who suffered from Alzheimer's disease and failed to recognise him. Alan had married a woman named Sally but they had no children. John saw no purpose in his life now that his family was gone.
He tried to commit suicide but Jack Harkness stopped him. After explaining himself, Jack decided to let him kill himself. He did so by carbon monoxide poisoning, sitting alongside Jack and holding his hand till his last breath (TV: Out of Time)