A police inquiry into one of the biggest scandals ever to rock British intelligence has recommended that two IRA veterans, one a key Sinn Féin figure, be charged, the Guardian has learned.

The pair are named in files sent by the head of Operation Kenova, the multimillion-pound investigation into “Stakeknife”, an army agent at the heart of the IRA during the Northern Ireland Troubles.

The charges recommended to be levelled at the pair, one of whom plays an important backroom role within Sinn Féin in Northern Ireland, are connected to the 1986 IRA murder of the Ulster loyalist paramilitary John Bingham.

The Belfast republican Freddie Scappaticci, alleged to be Stakeknife, the British army spy working at the heart of the IRA’s counter-intelligence unit, will also be charged in relation to the killing of Bingham, sources close to the Operation Kenova investigation have told the Guardian.

The Guardian can reveal that three civilian crown lawyers have also been recommended to be charged with perjury in connection to Scappaticci’s previous trials. The former IRA internee has consistently denied that he is Stakeknife.

An IRA unit shot Bingham, a UVF commander, dead at his home in the Ballysillan district after he directed a series of sectarian attacks against the Catholic community in north Belfast during the mid-1980s.

At least one of the other two men who are named by Jon Boutcher, the head of Operation Kenova and former chief constable of Bedfordshire, holds an “on-the-run” letter. These were in effect “get-out-of-jail” cards given to dozens of IRA fugitives and members wanted for past Troubles crimes.

Sources close to Operation Kenova have made it clear that Boutcher believes this man, who comes from west Belfast, can still be charged despite holding one of the letters. These were given by Tony Blair’s government as a secret concession to Sinn Féin during negotiations leading up to reaching a political settlement in Northern Ireland.

Boutcher’s naming of the other former IRA member who now works for Sinn Féin is, however, potentially a much more politically controversial move. This man has links to the current Sinn Féin leadership who promoted him through the party’s ranks.

It is understood Boutcher has made separate recommendations to the Public Prosecution Service (PPS) in Belfast that a number of people involved with Stakeknife should be charged with a total of nine murders.

The Guardian has seen text messages sent out by the Operation Kenova team to a number of relatives of those killed in IRA attacks. One of these messages from Boutcher to a relative confirms that “the case of John Bingham features as one of the files that has formed part of this submission. I recognise that as a result of this significant update you and your family may have a number of questions of me.”

In early 2018 Scappaticci was questioned under caution by Kenova detectives about Bingham’s murder. He again denied that he was the army super-spy they were investigating. Since that arrest, sources close to Operation Kenova say they have uncovered evidence that Stakeknife worked with two rogue Belfast loyalists who helped him “set up” Bingham for assassination. The two loyalists are said to have provided the IRA with information as to when their UVF target would be at his home.

What is the Stakeknife scandal, and what happens next? Read more

As well as the nine murders Boutcher has identified, the former chief constable has sent the names of three civilians, understood to be crown lawyers, to the PPS. In their cases, Boutcher is recommending that they be charged with malfeasance in public office, specifically perjury.

While a number of individual security force personnel are also recommended for prosecution by Boutcher and his team there will be no charges of corporate responsibility levelled at, for example, the Force Research Unit, the army intelligence branch that ran Stakeknife for decades inside the IRA.

One source close to Operation Kenova has warned that a decision on whether to act on Boutcher’s recommendations may take up to two years. They also point out that while there is “a strong evidential base” to proceed with charges, the final decision on whether to prosecute more than 20 people caught up in the Stakeknife scandal will rest with the attorney general.