Having previously coached Allan at Claremont, Gerard Neesham the inaugural Fremantle coach, targeted Allan to return to Western Australia. As the most experienced and highly decorated player in the initial 45 man squad, he was named Fremantle's first captain. He was the only former All-Australian, the only club best-and-fairest winner and one of only 2 former premiership players in the original Fremantle squad of 50 He played all 22 games in 1995 and finished 3rd in the best and fairest award. However injuries took their toll in 1996, restricting him to only 8 games for the year. In 1997 he relinquished the captaincy to Peter Mann and managed to play 17 games. However, a degenerative knee condition caused Allan to retire from football at the end of the 1997 season. He had played 145 AFL games in total, along with 66 for Claremont and 6 state games, earning him a position in the WA Football Two Hundred Club.
Coaching
Allan stayed at the club as an assistant coach in 1998. When it became clear Gerard Neesham would not coach Fremantle in 1999, Allan tendered his resignation pending the appointment of a replacement. When interviewed by new head coachDamian Drum, he was told no position would be available. His disappointment was obvious, telling the media Ironically, three years later Allan was called on as care-taker to replace Drum, sacked after the team's 10th consecutive loss, a diabolical performance against the Sydney Swans at the Sydney Cricket Ground in round 9, 2001. Despite his role three years previously as assistant coach, Allan did not view the appointment as leading to a permanent position. On being made coach, he told the media: Fremantle won two of the remaining 13 matches with Allan as coach and finished last on the AFL ladder. Allan the coach was demanding rather than inspiring and was openly critical of the playing group. At the press conference after a home loss to Port Adelaide he told the media:
"if they are looking for me to motivate them for the next eight weeks, they are barking up the wrong tree... clearly out there today we had too many out there today who haven't got strong enough character".
Nevertheless, a dispirited playing group stayed reasonably competitive in many of the remaining games of the season. Allan's two victories were both notable: the first was in Round 18 against at Colonial Stadium, which broke an 18-match, 370-day losing series of matches, and the second was in the final match of the season against. The joyous spirit of this game, played in front of a smallish but passionate crowd in night rain at Subiaco Oval, was rejuvenating for the club and its supporters after the gloom of the Damien Drum years. The new optimism was built on with the appointment of the new coach for 2002, Chris Connolly, and the exciting victories and growing crowds that and the subsequent years brought.
Allan has had an active media career in print, on radio and on TV, including The West Australian, ABC Radio, 6PR, SEN and the now defunct Fox Footy Channel. Outside of football he has become a successful businessman in the Margaret River wine industry. In 2005 he was elected to the Members position on the board of the Fremantle Football Club. He will hold that position for 2 years before all Fremantle Season Ticket holding members over 18 years vote again. In March 2012, Allan was inducted into the West Australian Football Hall of Fame. He is the first former player to be inducted.
