Connor continued to inspire Rovers to success on their return to the Premier Division and they finished fifth that year. The club also enjoyed its first significant cup run in a decade and faced Derry City in a home semi-final which finished all square in front of one of the biggest crowds the Showgrounds had seen for a long time. The replay would prove to be a disaster, however, with Rovers losing 5–0 on 31 October 2006 in the Brandywell. Shortly after Connor stunned the club by announcing his departure to join Bohs before the season had even ended. His departure left a lot of resentment towards him in Sligo which remains to this day. His replacement, Rob McDonald, a former PSV Eindhoven player would only last one game in charge, that being the final game of the 2006 season. He was sacked only a couple of weeks before the new season was to begin which left Rovers in the temporary control of caretakers Leo Tierney and Dessie Cawley as the new season began until a new man could be appointed.