Allison's next head coaching job came in 1999–2000 with the Fort Wayne Komets of the UHL, leading them to a 40–27–7 record and a trip to the third round of the playoffs. He returned to the IHL as coach of the Milwaukee Admirals, the Nashville Predators IHL affiliate, leading the team to a 42–33–7 record, but losing in the first round of the playoffs. He moved with the club to the AHL in 2001–02, but missed the playoffs with a 30–35–10–5 record.