A claim that the Reverend Ian Paisley funded a UVF bomb attack on a reservoir, threatening the water supply to Belfast, is set to be aired by the BBC.
The new programme is also set to screen archive footage of Martin McGuinness showing a gun to children.
The examination of the pasts of Northern Ireland’s former first and deputy first ministers, now both deceased, come in the first instalment of a new seven-part BBC Northern Ireland series marking the 50th anniversary of the start of the Troubles.
Spotlight On The Troubles: A Secret History, probes the earliest days of Northern Ireland’s Troubles using clips of previously unseen footage, formerly classified documents and new testimony.
The first instalment, presented by Darragh MacIntyre, traces the heightening unrest between Protestants and Catholics in the late 1960s and the birth of the civil rights movement.
It examines attempts by then prime minister Terence O’Neill to liberalise discriminatory practises against fierce opposition from Rev Paisley.
In the programme, David Hancock, a former soldier, claims a police officer told him that the Rev Paisley supplied funding for the bomb on the Silent Valley reservoir, which was the main water supply for Belfast.
The blast was one of a series carried out by Loyalists between March and April 1969 targeting water and electricity installations.
They were initially blamed on the IRA before it emerged that Loyalists were responsible.
Rev Paisley was in prison at the time of the Silent Valley bomb on April 21, 1969, for organising an illegal counter-demonstration.
Mr O’Neill resigned following the resulting political crisis.
The programme also exhibits a formerly classified government document which reveals how the Rev Paisley’s speeches and sermons were recorded in an effort to prosecute him, as well as police records from the time which drew links between him and the UVF.
Rev Paisley, who died in 2014, consistently and strongly denied any link with any paramilitary group during his life.
The Rev Ivan Foster, a colleague of Rev Paisley at that time, distanced the movement against Mr O’Neill from Loyalist violence, telling the programme while men from the UVF may have attended their protests, acts of violence were wrong.
The Spotlight programme also shines new light on the late Martin McGuinness’ involvement with the IRA.
Mr McGuinness admitted to being a member of the IRA while giving evidence to the Bloody Sunday Inquiry.
The programme shows archive footage of the IRA assembling a car bomb in Londonderry.
Former IRA member Shane Paul O’Doherty identifies a man walking in the clip as Mr McGuinness.
Footage is also shown of Mr McGuinness sitting in a car showing a gun to children.
The arrival of the army in Northern Ireland to relieve a riot weary RUC is also explored in the 90-minute programme, and how soldiers were first welcomed by nationalists before becoming reviled, as well as the controversial introduction of internment, collapse of the Stormont parliament and some of the most poignant murders of the early Troubles.
Later in the series, the Spotlight team will investigate early attempts to end the conflict, the secret intelligence war against the IRA, the role of Loyalists in the violence, collusion and the path to peace.
Mr MacIntyre said the challenge for him was to “bring new material to light which might in turn give a new or better understanding of what happened here”.
“We had of course an awful lot of help in where to look for new material – from those many journalists and historians who themselves have turned over so much of the ground that we planned to travel. But at a certain point it was down to us, the team working on the project, to search on more time in the box of files, to knock one more door, to make one more phone call, to make sure that we had done our earnest best to get to the truth,” he said.
“But I have no illusions, a huge distance has yet to be travelled before anyone gets anything like the full story of what happened here. That journey may never be finished.”
Spotlight On The Troubles: A Secret History will be shown on BBC 1 Northern Ireland and across the UK on BBC 4 on September 10 at 8.30pm.