Seamus Daly was living "under the radar" close to the Irish border before being arrested at a shopping centre car park in Newry, Co Down, prosecutors claimed.
As he was refused bail it was confirmed that charges were brought based on a review of available evidence rather than any new material.
The case against him centres on telephone analysis allegedly linking him to the outrage.
A former business associate who says he spoke to him on a mobile believed to have been used by the bomb team is a "pivotal" prosecution witness, a judge was told.
Daly faces 29 counts of murder over the August 1998 Real IRA attack.
The 43-year-old bricklayer, originally from Cullaville, Co Monaghan, but now residing in Jonesborough, Co Armagh, also faces counts of causing the explosion in Omagh and possession of a bomb in the Co Tyrone market town with intent to endanger life or property.
He is further charged with conspiring to cause an explosion and having explosives with intent in connection with a separate dissident bomb plot in Lisburn, Co Down in April that year.
No one has ever been convicted in a criminal court in connection with the atrocity.
But Daly, who has a previous conviction in the Irish Republic for IRA membership, has already been found liable for the bombing in a landmark civil action taken by victims' families.
One of the bereaved, Michael Gallagher, whose son Aidan died in the blast, was in court as he appeared by a prison video link to seek bail.
The court heard that a man named Denis O'Connor claims Daly phoned him on the day of the attack using a mobile suspected of having travelled into Omagh on the bomb run.
Cell-site analysis also allegedly links him to the earlier bomb incident at Lisburn involving a similar modus operandi and warnings.
Asked by the judge if any of the information was new, prosecution counsel Kate McKay confirmed it was already known to police.
She contended, however, that there have been difficulties in locating Daly before he was detained on 7 April.
He gave police a false name - believed to be that of his brother - and incorrect address.
Opposing bail, Mrs McKay claimed the chance to arrest him only emerged when he left his home.
"Police believe he has been residing in that address almost keeping under the radar," she said.
Questioned on how long detectives had been looking for him, she replied: "Police would say in the region of five years."
Throughout four days of interviews Daly made no comment to all questions.
In a pre-prepared statement, he denied being a member of the IRA or any involvement in either the Lisburn attempted bombing or the attack on Omagh, which killed 29 people including a woman pregnant with twins.
Defence counsel Dermot Fee QC argued that the case against his client is too weak for criminal charges.
"There's been no additional evidence in 14 years," he said.
"It has been undoubtedly analysed and undoubtedly conclusions reached (previously) that there was insufficient evidence. Nothing has changed from that."
Mr Fee contended that it was "ridiculous" for the prosecution to suggest Daly's no-comment interviews marked a development in the case.
Rejecting any suggestion that the accused had been evading the authorities, the barrister said he has been in Northern Ireland for nearly three years.
"He's just been living a normal family life at that location," he added.
However, Mr Justice Treacy held that the prosecution had established a reasonable suspicion against Daly.
Bail was refused due to the twin risks the accused may commit other serious offences or flee.
The judge pointed to Daly's decision not to appear at any stage during the civil case against him and three other men held liable, and added: "I also take into account the prosecution contention that they have been looking for the applicant for five years."