Paul Greaney KC outlined the “working hypothesis” of the inquiry when it resumed its latest phase on Monday.
In 2009, a judge ruled that four men – Michael McKevitt, Liam Campbell, Colm Murphy and Seamus Daly were all liable for the Omagh bomb.
A fifth man, Seamus McKenna, was acquitted in the civil action and later died in a roofing accident in 2013.
In a statement to the inquiry, sitting at Bradford Court in Belfast, Greaney named McKenna, Daly and Murphy as among the 14 people linked to evidential activity.
Greaney told the inquiry: “The evidence suggests Colm Murphy sat like a spider in the centre of the web of the plan to detonate a bomb in Omagh.”
Referring to the civil case, Greaney said that the fact that McKenna “was not found liable is not an outcome which binds this inquiry”.
“Our working hypothesis is that, contrary to that finding, he played a key role,” he said.
The use of telecommunications is a key part of the evidence in front of the inquiry and some of the most frequently referred to mobile phones have been assigned colours for ease of following their links.
The inquiry heard how it was “likely” that the Vauxhall Cavalier car used in the bombing was “stolen to order” in the days before the bombing.
Evidence was outlined that on 14 August 1998, the day before the bombing, a “test run” of the journey to the bomb site was carried out in a Volkswagen Golf car.
