The high-security prison in New York City where 9/11 mastermind Khalid Sheikh Mohammed is expected to be sent to await his trial has a supermax wing to keep even the most notorious criminals quiet — but it isn't perfect. Just ask Louis Pepe.

Ten months before Al Qaeda in 2001 struck a deathblow in the heart lower Manhattan, one of the terrorist group's founding members plunged a sharpened comb through Pepe's left eye and into his brain, blinding the 42-year-old prison guard and causing severe brain injuries that plague him to this day.

Pepe told FoxNews.com he worries that sending Mohammed and four of his alleged fellow 9/11 conspirators to New York could compromise the safety of the guards at the MCC prison. Keeping the prisoners in one location, he said, was especially dangerous.

"Could you imagine over there what they're gonna do, God forbid?" asked Pepe, now 52, who lost feeling in the right side of his body and most of his ability to speak. "After all these years, you'd think they should know."

On Nov. 1, 2000, Pepe was ambushed in the cell of Mamdouh Mahmud Salim — an alleged top aide to Usama bin Laden. Salim's cellmate, another Al Qaeda suspect, joined in the attack, which prosecutors say was an attempt to steal Pepe's keys to the cell block to free other prisoners and take hostages.

The two had been granted permission by a federal judge to purchase hot sauce, says Pepe's sister, which they then stored in a honey jar and used to create a blinding mace. Teaming up against Pepe, they beat and blinded him, covering the floor in his spattered blood. They then tried to rape him as he waited an entire hour for fellow guards to come to his aid, his sister said.

"They wanted to discredit the badge and what he stood for," Eileen Trotta told FoxNews.com. "After they plunged him in the eye with that makeshift knife, they did the sign of the cross on his chest."

Trotta said it would be like "deja vu" to see more Al Qaeda detainees shipped into New York for trial, where their court hearings will be just blocks from Ground Zero

"There's no reason why everything has to be in New York, especially after 9/11 and what happened to Louis," she said. "It doesn't make sense — why bring them into the hotbed of the city?"

The Obama administration announced Friday morning it was ending the military commissions that were trying Khalid Sheikh Mohammed and his four co-defendants at Guantanamo Bay, and would transfer them into civilian courts — and out of the military prison complex that has kept them confined for the better part of a decade.

The federal Bureau of Prisons, which administers the MCC complex in New York, said the jail has long housed "some of the most dangerous offenders" in the nation — and housed them safely. Accused terrorists linked to Al Qaeda plots are currently being held in cells on "10 South," the prison's notorious 10th floor, where the convicted leaders of the 1993 bombing of the World Trade Center were held during their trial.

New York Mayor Michael Bloomberg said he supported the Obama administration's decision to bring the suspects to New York to face justice near the World Trade Center site where so many New Yorkers were murdered.

"I have great confidence that the NYPD, with federal authorities, will handle security expertly," Bloomberg said. "The NYPD is the best police department in the world and it has experience dealing with high-profile terrorism suspects and any logistical issues that may come up during the trials."

The Bureau of Prisons said the attack on Pepe was nearly unique and that the prison's highly trained staff are prepared for any class of criminal.

"That was an extraordinarily brutal attack and I don't believe they've experienced anything like that since then," said Traci Billingsley, a spokeswoman for the bureau.

Billingsley said she could not discuss whether security measures have changed since Pepe was nearly killed in 2000, nor could she discuss whether any new steps would be taken if more Al Qaeda suspects are sent to the MCC.

But those reassurances were little consolation for Pepe and his sister, who said the government was quick to forget the terrible lesson of his attack.

"We're such a lax country — we don't learn from our mistakes," Trotta told FoxNews.com. "We have to protect our own, and at this point we're not doing it.

"After almost 10 years I'm still seeing my brother struggling very hard to have some kind of semblance of life."