Despite being drafted to the VFL, the West Torrens Football Club of the Adelaide based SANFL argued that Long was "contracted with the club and could not play anywhere else." "I was guaranteed this wasn't the case, so I took the contract to Darwin and met with Michael's father Jack and he was irate. He grabbed it and wrote the word 'bullshit' right across the front of it. When it became clear he wanted to play at Essendon, West Torrens agreed it wasn't a binding contract", Judkins said.
Long played perhaps the best game of his career in the 1993 AFL Grand Final. Playing on Mark Athorn, Long ran amok, helping Essendon gain a healthy quarter-time lead, and to maintain it. By the end of the game, he had amassed 20 kicks and 13 handballs, totaling 33 possessions.
In the pre-season of 1994 in a practice match against the West Coast Eagles, Long injured his knee which required 12 months of solid rehabilitation, and he was not seen for the entire 1994 AFL Home and Away season.
The AFL arranged a mediation session between Long and Monkhorst and although Long was clearly unsatisfied by the short-term outcome of this meeting, long-term it set a precedent and since this incident, there have only been three widely publicised accusations of racial taunts on the AFL field.
For the next two seasons he needed knee surgery and only took the field seven times. He missed the first half of 1998 recovering from the surgery, but finished the year strongly playing in nine games.
According to the round 3 AFL Record of 1999, between the beginning of the 1994 and end of the 1998 seasons, Long played only 38 of a possible 119 games.
Long had the honour of kicking the first ever goal at the new Docklands Stadium when it opened in 2000. He was also a member of Essendon's record-breaking premiership team in 2000 which saw only one loss for the entire season. Long faced heavy scrutiny for his bump on Troy Simmonds, which rendered Simmonds unconscious and raised the possibility of him losing mobility – which fortunately never eventuated. However, this incident inspired the AFL to introduce new rules protecting players with their heads over the ball. Long was suspended for this incident.
2001 was Long's final season and although Essendon made the Grand Final that year, Long aggravated a hamstring during grand final training and was forced to name himself unavailable on the eve of the game, which Essendon lost to the Brisbane Lions who would go on to win three straight premierships.
Following his retirement, Long became a spokesman for Indigenous Australians. He was also a critic of then Prime Minister John Howard's policies towards Indigenous Australians – most notably Howard's refusal to make an apology to the Stolen Generation. In a letter published in Melbourne's The Age, Long likened Howard to 'those cold-hearted pricks' who stole his parents. His political activities culminated in a protest march from Melbourne to Canberra, Australia's national capital. The aim of the walk was to obtain a meeting with the Prime Minister. After ten days of intense media scrutiny of the walk, the Prime Minister eventually granted Long a meeting who called an end to the walk, having completed about 325 km of the planned 650 km walk.
In 2006 he was charged with assaulting a man at a football club function. He pled guilty but no conviction was recorded.
In July 2011, Long signed up as the latest ambassador for weight loss agency Jenny Craig. Weighing 112 kg, 30 kg more than his playing weight, his aim was to drop at least 10 kg in around 10 weeks. In September 2011 on The Footy Show, he announced he had smashed his goal, losing 17 kg in 10 weeks.