Obama met with relatives of Cole sailors and 9/11 victims Friday in the wake of three executive orders he signed last month ordering the closing of the military prison at Guantanamo Bay, where the alleged mastermind of the attack is being held.
The deadly strike is considered a seminal event in the days leading up to 9/11. Seventeen American sailors were killed off the coast of Yemen Oct. 12, 2000, when a suicide bomber rammed his boat into the hull of the Cole.
As the Obama administration prepares to review the cases of the 245 detainees held in Guantanamo, the president called in the concerned families to explain his plan to prosecute the detainees outside of military courts.
Some of those present at the meeting have criticized Obama's plan to close the prison, and looked for reassurance that they will see justice served after years of waiting. The family of Cherone Gunn, a 22-year-old seaman killed on the Cole, broached the subject of opening an investigation.
Gloria and John Clodfelter, the parents of sailor Kenneth Clodfelter, who lost his life in the attack, were at Friday's meeting with the president and said they also support the idea of an investigative commission for the Cole.
"All of the families were extremely positive about [it]," said John Clodfelter, noting that families felt it was long overdue. "It's something that should have been done within a year of the attack."
According to three sources at the closed-door conference, the president was warned by a member of the Cole contingent that a commission would be unpopular with the Navy and would require investigating the Clinton administration's actions against Al Qaeda. That could be politically tricky -- one democratic administration investigating the possible intelligence failures of another democratic administration.
But Clodfelter, who harbored reservations before the meeting, said he believed the president was not afraid to navigate the thorny territory.
"If you've done something wrong, you've done something wrong regardless of who it is -- Republican, Independent, Democrat, whoever," Clodfelter told FOX News. "This is the one president who really seems like he's willing to go ahead and do something."
The tale of the USS Cole is one of frustration. The bombing occurred in the final months of the Clinton administration and less than a year before 9/11. Some Cole families complain that the Clinton administration never took action and that the Bush administration viewed the attack as one that didn't happen on its watch.
But this was not the first attempt on a U.S. Navy vessel in the Persian Gulf in 2000. Nine months before the Cole attack, another ship was in Al Qaeda's crosshairs.
On Jan. 3, 2000, Al Qaeda launched a nearly identical but unsuccessful attack on USS The Sullivans. Former senior Defense official Cully Stimson, now an analyst for the Heritage Foundation, says the operation was a disaster for Al Qaeda.
"They put so much explosives on the boat that it sank in the harbor," Stimson said. "If it wasn't so damn serious it would have been a Laurel and Hardy-type scenario."
Saudi national Abd al-Rahim al-Nashiri, who is still being held at Guantanamo, is now seen as the central link between the two plots, which both targeted the U.S. Navy off the coast of Yemen. Al-Nashiri was careful not to repeat the mistakes of the first plot, according to Stimson.
"They learned the weight to mass ratios with respect to the boat and its capacity. Essentially, that bombing was the dry run for the Cole bombing."
The 9/11 commission report is not silent on the Cole strike or that of The Sullivans. By December 2000, the CIA had developed a timeline linking the two events, but only after the Cole was already hit. Some Cole families question whether the ball was dropped -- whether critical intelligence was missed or misinterpreted.
A senior administration official told FOX News that President Obama has not ruled out the idea of a 9/11-style commission on the Cole attack, and it is now under review.
Despite hearings on Capitol Hill and three military investigations of the attack, some of the Cole families are still not satisfied, and no one has been held accountable for the killings.
Now with the closing of the military prison at Guantanamo, where the chief suspect is being held, old wounds have been reopened.
"Remember that our military people are not cannon fodder to just be thrown out there. They are there to protect us," said Clodfelter. "Our military people are treated badly. They deserve every bit of our respect. It's not being done."