In February 1996, Cook was sold to Tranmere Rovers for £250,000. Whilst at Tranmere, he became a key member of the side, playing 60 league games in just eighteen months. In October 1997, Tranmere accepted a bid of £250,000 from Stockport County and regained the fee initially paid for Cook. After twelve months at County, Cook began to be regarded as 'too old', despite only being 32. This led to Cook making a loan move to Burnley before making the move permanent in July 1999. After a falling out with Burnley manager Stan Ternent, Cook went on loan to his former club Wigan Athletic, but made just six appearances before he was re-called to again take his place in the starting line up at Turf Moor. Cook left Burnley at the end of the 2002/03 season, alongside teammate Andy Payton. The two players received a standing ovation from the fans for their contributions to the club. Cook signed for non-league side Accrington Stanley and went on to become a first team regular in their push for promotion to the Football League. This target was finally achieved in the 2005/06 season when Stanley were crowned as Champions of the Conference. After achieving this aim, Cook retired after 643 league appearances for nine different clubs. After the end of the 2005/06 season, Cook was granted a testimonial by Accrington as a sign of appreciation for his efforts. The testimonial was played on 2 May 2006 at the Interlink Express (now the Wham) Stadium; Accrington against a Burnley Select XI featuring old teammates Dean West, Lenny Johnrose, Ian Cox, Kevin Ball and Cook's son Liam. Management career Southport Cook was appointed manager of Conference side Southport on 13 June 2006, a post he was sacked from in January 2007 following defeat at Northwich Victoria. Sligo Rovers On 27 April 2007, Cook was appointed manager of Sligo Rovers taking over from Rob McDonald, who resigned before the start of the season. During Cook's unveiling, he stated that he was from Liverpool and that he will not have anything to do with any journalist from the Irish Sun, (due to the articles printed about Liverpool supporters during the Hillsborough disaster). He led Rovers to a 6th place league finish in his first season in charge. Cook's second season saw him guide the bit o' red to fourth in the league and thus secure a UEFA