He was with the club in this role for four years, progressing to being Dalglish's right-hand man as the team (still containing, and now captained by, Hansen) won the League in 1988 and 1990 and the FA Cup in 1989. Thompson was working at the club at the time of the Hillsborough disaster, on 15 April 1989 at the beginning of the FA Cup semi-final against Nottingham Forest. The tragedy claimed 94 lives on the day, with the final death toll reaching 96. An abiding image of Thompson the coach came in the 1989 FA Cup final against Merseyside rivals Everton when a last minute chance for Everton to equalise went awry, and the camera caught Thompson, sweating in his suit and tie, sitting on the Wembley bench while shaking his fists in relief, delight and anticipation. Everton did equalise moments later and forced extra-time, which Liverpool eventually won.