Adair was expelled from the organisation in 2002 following a violent power struggle. Since 2003, he, his family and a number of supporters have been forced to leave Northern Ireland by other loyalists.
The Provisional Irish Republican Army (IRA) bombing of a fish shop on the Shankill Road in October 1993 was an attempt to assassinate Adair and the rest of the UDA's Belfast leadership in reprisal for attacks on Catholics. The IRA claimed that the office above the shop was regularly used by the UDA for meetings and one was due to take place shortly after the bomb exploded. The bomb went off early, killing one of the IRA men (Thomas Begley) and nine Protestant civilians. The UFF retaliated with a random attack on the Rising Sun bar in Greysteel (County Londonderry), which killed eight civilians, two of whom were Protestants. Adair has survived 13 assassination bids, most of which were carried out by the IRA and Irish National Liberation Army.
During this time, undercover officers from the Royal Ulster Constabulary had recorded months of discussions with Adair, in which he boasted of his activities, producing enough evidence to charge him with directing terrorism. He was convicted and sentenced to 16 years in the The Maze prison.
Adair was held with other loyalist prisoners in their "block" of the Prison. In prison, according to some reports, Adair sold drugs such as cannabis, ecstasy tablets and amphetamines to other loyalist prisoners, earning him an income of £5000 a week.
In January 1998, Adair was one of five loyalist prisoners visited in the prison by British Secretary of State for Northern Ireland, Mo Mowlam. She persuaded them to drop their objection to their political representatives continuing the talks that led to the Good Friday Agreement in April that year. In 1999, Adair was released early as part of a general amnesty for political prisoners after the Agreement.
In 1999, shortly after his release from prison, Adair was shot at and grazed by a bullet in the head at a UB40 concert in Belfast. Adair blamed the shooting on republicans, but it is thought that rival loyalists were to blame.
In August 2000, Adair was again mildly injured by a pipe bomb he was transporting in a car. He again attempted to blame the incident on an attack by republicans, but this claim was widely discounted. A feud had broken out at that time between the UDA and the Ulster Volunteer Force (UVF) leaving several loyalists dead. As a result of Adair's involvement in the violence, the then Secretary of State for Northern Ireland, Peter Mandelson revoked Adair's early release and returned him to prison.
In May 2002, Adair was released from prison again. Once free, he was a key part of an effort to forge stronger ties between the UDA/UFF and the Loyalist Volunteer Force (LVF), a small breakaway faction of the UVF loyalist paramilitary organization in Northern Ireland. The most open declaration of this was a joint mural depicting Adair's UDA "C company" and the LVF. Other elements in the UDA/UFF strongly resisted these movements, which they saw as an attempt by Adair to win external support in a bid to take over the leadership of the UDA. Some UDA members disliked his overt association with the drugs trade, which the LVF were even more heavily involved with. A loyalist feud began, and ended with several men dead and scores evicted from their homes.
On 25 September 2002, Adair was expelled from the UDA/UFF along with close associate John White, and the organisation almost split as Adair tried to woo influential leaders such as Andre Shoukri, who were initially sympathetic to him. There were attempts on Adair's and White's lives.
Adair returned to prison in January 2003, when his early release licence was revoked by Secretary of State for Northern Ireland, Paul Murphy, on grounds of engaging in unlawful activity. On 1 February 2003, UDA divisional leader John Gregg was shot dead along with another UDA member (Rab Carson), on returning from a Rangers F.C. match in Glasgow. The killing was widely blamed on Adair's C Company - Gregg was one of those who had organised the expulsion of Adair from the UDA. Five days later, on 6 February, about 20 Adair supporters, including White, fled their homes for Scotland, widely seen as a response to severe intimidation.
The police in Bolton have questioned his wife, Gina about her involvement in the drugs trade, and his son (nicknamed both 'Mad Pup' and 'Daft Dog' ) has been charged with selling crack cocaine and heroin. Adair himself was arrested and fined for assault and threatening behaviour in September 2005. He had married Gina Crossan, his partner for many years and the mother of his four children, at the Maze Prison on 21 February 1997. She is three years Adair's junior and grew up in the same Lower Oldpark neighbourhood.
After being released, he was almost immediately arrested again for violently assaulting Gina, who suffers from ovarian cancer. Since this episode Johnny Adair is reported as having moved to Scotland, living in Troon in Ayrshire.
In May 2006, it was reported that Adair had received £100,000 from John Blake publishers for a ghost-written autobiography.
Johnny Adair appeared in a documentary screened in 2007. The documentary was made by Donal MacIntyre/ The focus of the film centered around Adair and another supposedly reformed character, a Neo Nazi from Germany called Nick Greger, and their trip to Uganda to build an orphanage. Adair was seen to fire rifles, stating it was the first time he had done so without wearing gloves. Adair also admitted to being "worried sick" and "pure sick with worry" after Nick disappeared in Uganda for days on end. It turned out that Nick had gone off and married a Ugandan lady. Adair confessed via telephone that he "thought something might have happened to Nick".