The 2000–01 season started early for Bradford after chairman Geoffrey Richmond decided to enter the Intertoto Cup. Wetherall did not play in the team's first game away at FK Atlantas, and after playing in the second leg and the two third-round games, he missed the semi-final with Zenit St Petersburg because of an ankle injury. Bradford subsequently lost both legs. Wetherall started the league season but after playing all 52 league games since joining Bradford without leaving the field, Wetherall limped off before half-time during a 2–0 defeat to their nearest rivals Derby County in November 2000. Days after new manager Jim Jefferies took over, Wetherall was ruled out until the following February following a groin operation. His first game back was on 24 February 2001 as Bradford lost 2–1 to West Ham United. His return to league action lasted just four games when, after scoring in a 2–2 draw with Newcastle United, he was ruled out for the rest of the season with a recurrence of the groin injury. Bradford lost their Premier League status a month later after losing 2–1 at Everton.