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Muir was signed to Tranmere Rovers by player-manager, Frank Worthington, who was his striking partner in his first season at the club. Despite his evident promise, he spent his early career at Rovers immersed in struggle, as the club languished in the basement of the league and Muir was part of the side that beat Exeter City 1–0 to save Rovers from automatic relegation from Division Four in 1987. He set up the crucial goal, headed in by Gary Williams in the 77th minute of the last game of that season. Muir prospered when new manager, John King, signed a big target-man, Jim Steel, as his strike partner in late 1987. Within four years, Rovers had been promoted twice and appeared at Wembley five times, with Muir scoring in the FA's centenary celebrations in 1988 and in Tranmere's Leyland DAF Trophy victory over Bristol Rovers in 1990. Injury prevented Muir partaking in the final strait of Rovers' promotion run in 1991 when they reached the second tier of English football for only the second time in their history. That summer, the signing of John Aldridge at Tranmere led to the marginalisation of Ian Muir, who remained a regular goalscorer when called upon for the remainder of his Tranmere career.
To a generation of Tranmere Rovers fans, Ian Muir is remembered as a legendary player, who played the starring role in the greatest period of the club's history and also the finest centre forward not to have played in the top tier of English football.