Scott's managerial career started to flower during his time at Dunfermline and Aberdeen, where he was in joint control with Alex Smith, but it was at Dundee that his reputation as a boss was forged. He took over at Dens Park in March 1998 and in his first full season guided the club back into the Scottish Premier League and steered them to the sanctuary of mid-table. His time in charge came to an abrupt end, as he was forced out of the club in the summer when a consortium, headed by Italian Ivano Bonetti, took over at Dundee.
Following his acrimonious departure he headed south to try his luck in the English league after being appointed the successor to Gary Brazil at Notts County. He took the helm in June 2000, and made an encouraging start, helping The Magpies into a position where they can challenge for a play-off place in his first season in charge.