He was one of their most popular members. Kieran Doherty rose rapidly through Real IRA ranks, becoming OC (officer commanding) of the prisoners in Portlaoise when he was just 24.

He was serving a six-year sentence for armed robbery. He did his time easily. I interviewed him in 2004 as the prisoners embarked on a 72-hour hunger-strike in protest at conditions.

His comrades nicknamed him 'Goggles' and 'Harry Potter' because of his thick spectacles. He enjoyed the banter. In jail he met Séamus McGreevy (56) from Co Meath, a founder Real IRA member jailed for running an underground military training camp. They became like father and son.

When Doherty was released from prison, he rejoined the Real IRA in his native Derry, becoming a senior member of its GHQ staff. In February, the Real IRA abducted and killed him. His body was dumped near the Donegal border. Three weeks earlier, Séamus McGreevy had hung himself.

The two deaths were linked but it was Doherty's murder which caused shockwaves. In a scene which many people had hoped belonged to the past, he was discovered lying on the road stripped to his boxer shorts, his hands tied, with two bullets fired into the back of his head. He was 31 years old.

At Massereene, the Real IRA branded the two men delivering pizzas to British soldiers as "legitimate targets" and tried to kill them. Now, the organisation was showing equal ruthlessness to one of its own.

A Real IRA Army Council representative told the Sunday Tribune that Doherty had admitted his involvement in a €500,000 cannabis factory uncovered by gardai in Co Donegal in January. Doherty's family strongly deny this, accusing the Real IRA of lies.

The murder shows the Real IRA's iron-fisted internal discipline and its utter lack of mercy towards anyone it believes guilty of 'betrayal'. The horrific series of events, which would result in the death of two senior Real IRA members, began in a house near Carrigans, Co Donegal.

Séamus McGreevy had built the house but couldn't sell it because of the property market slump. He asked Doherty to rent the house to tenants and act as caretaker.

McGreevy had come into a very substantial sum of money when a motorway was built through his farmland in Co Meath. Republicans say he gave most of this to the Real IRA and also to ex-prisoners struggling financially.

"Séamus was a very trusting, quiet countryman with deeply-held republican beliefs," a friend says. "He was extremely generous." Sources say McGreevy had given Doherty cash to set up a café for himself in Derry but the venture had failed.

When gardai uncovered the cannabis factory at the Donegal house, of which Doherty was caretaker, McGreevy was distraught. "He was horrified his property was linked to drugs," a friend says. "He took it very badly."

McGreevy was already under pressure, fighting extradition to Lithuania where he was wanted in connection with an alleged Real IRA guns smuggling plot. After the drugs
factory was discovered, the Real IRA took swift action.

The Army Council spokesman says: "We began a six-week investigation. The IRA stood down its entire Derry brigade pending the outcome of our investigation. An outside IRA security team moved in to carry out the inquiry. It was an extensive investigation during which many witnesses, including members of the criminal gang involved in the drugs' factory, were interviewed.

"Those individuals gave statements saying Kieran had been integrally involved in setting up the whole operation and had actually sourced the cannabis plants." The spokesman claims Doherty was "interviewed" twice before the night of his murder.

Once, at a paramilitary "court of inquiry", Doherty denied the allegations. The Real IRA then held a "court martial" at which Doherty was "defended" by a Real IRA representative of his choosing "in keeping with the green book (traditional IRA rule-book)".

The spokesman claims that when Doherty was shown the statements from some of the criminal gang members, he then admitted involvement. The Real IRA says that at both "interviews", Doherty was ordered not to discuss the matter further nor to contact other Real IRA members.

On Bloody Sunday, 31 January, the Real IRA says Doherty phoned Séamus McGreevy who was having lunch at his sister's house. After the conversation, McGreevy left immediately. "He returned to his own home in Gormanstown and fed the cattle. Then he shaved, showered, put on his best suit and hung himself from a door-frame," a friend says.

"Whatever Kieran said led to Séamus hanging himself," the Real IRA spokesman says. The Real IRA believes McGreevy had "no involvement whatsoever" with the drugs. As Doherty's relatives point out, the Real IRA's summary justice mean he isn't here to defend himself. But even if its version of events is true, why did the Real IRA act so ruthlessly?

Doherty could simply have been ordered out of the country. Other "sanctions" traditionally used by republicans include a 'six-pack' where the victim is shot in the elbows, knees and ankles.

While the Provisional IRA shot dead activists it claimed were informers, it didn't kill serving members allegedly involved in drugs or crime. Even suspected sex offenders connected with the movement, as recent cases show, were at most sidelined or moved to another area. The Provisionals were far harsher on people outside the movement than on those within their own ranks.

The Real IRA operates by different rules. In January, it had shot dead a heroin dealer in Cork. It had also taken action against drug gangs in the North. So even if Doherty's alleged involvement was only with cannabis, the Real IRA believed this weakened it as an organisation and would lead to others accusing it of "double standards" on drugs.

"We couldn't be involved in taking action against others while turning a blind eye, or meting out a token punishment, to one of our own members involved in the drugs trade," the spokesman says.

Another reason also motivated the murder. In Real IRA eyes, Doherty had potentially compromised himself – and therefore the entire organisation – with the security services. He was open to blackmail by MI5.

The Army Council spokesman alleges MI5 "played some role" in the drugs factory which had been set up "to blacken the IRA's name and link us to the drugs trade which we abhor and oppose".

The organisation's suspicions focus on an individual who, with Doherty, allegedly initiated the cannabis factory idea.

Kieran Doherty's murder was part of a very murky world: the secret battle for supremacy that goes on every day between British intelligence and republicans.