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An 84-year-old Catholic nun will spend nearly three years in federal prison for breaking into one of the U.S. government's most secure facilities and helping deface a uranium-processing building with human blood, a federal judge ruled Tuesday.

Megan Rice, who turned 84 on Jan. 31, and fellow anti-nuclear activists Michael Walli, 64, and Greg Boertje-Obed, 58, were convicted in May of sabotaging the plant in Oak Ridge, Tenn. All three are members of the Plowshares movement of Christian pacifists.

U.S. District Judge Amul Thapar in Knoxville, Tenn., sentenced Rice to 35 months in prison for her role in the July 28, 2012, break-in and protest. The judge sentenced Walli and Boertje-Obed both to five years and two months in prison. Previously, Thapar had ordered the trio to pay nearly $53,000 in restitution for damaging U.S. government property.

In addition, Walli and Boertje-Obed will have three years of supervised release after their prison terms. The two men received longer sentences based on their past criminal history.

MORE: Snow delays sentencing

VIDEO: Protesters vandalize Y-12 building

During a four-hour hearing Tuesday, Rice pleaded with the judge not to grant her leniency.

"Please have no leniency on me," she said. "To remain in prison for the rest of my life would be the greatest honor you could give me."

Thapar didn't oblige but did say that breaking the law isn't the right way to pursue political goals. He said he hoped that a significant prison sentence would deter others from following the same path and bring them "back to the political system I fear that they have given up on."

The protesters picked late July 2012 to break in to the Y-12 National Security Complex because it was close to the dates when the United States dropped atomic bombs on Hiroshima and Nagasaki, Japan, during World War II.

The three cut through fences and made it through multiple layers of security. They spent more than two hours in a restricted area and had time to splash blood on the outside of the building where the government processes weapons-grade uranium before security personnel apprehended them.

The fallout from the break-in was swift. The incident prompted the Department of Energy to take immediate action. It increased patrols and removed the guard force's general manager and two of his key staff.

Congress had hearings and newly appointed Energy Secretary Ernest Moniz called the break-in unacceptable. Security experts have said the breach raised questions about not only about how the nation protects its nuclear weapons and materials but also how private companies secure civilian sites such as nuclear-power plants.

The three have garnered worldwide attention. Thousands of letters of support have poured into the court from around the world. Those include letters from groups such as the Union for Concerned Scientists.

While acknowledging the three were convicted of a federal crime, they exposed serious security weaknesses at Y-12, the group said.

Edwin Lyman, a nuclear security expert at the Union of Concerned Scientists, said in January that the protesters did the nation a public service.

Tuesday, the trio who broke into what was supposed to be one of the most secure buildings in the world will learn how long they will spend behind bars. 2-17-14

"We think, even though they were convicted of a federal crime, there are mitigating circumstances and they made the country safer," Lyman said.

The government has taken the case seriously. The three have been in custody since their conviction, and prosecutors recommended sentences of six to nine years.

A key issue Tuesday was how the judge should follow federal sentencing guidelines. Lawyers for the activists that argued the time they already have served is sufficient punishment.

At the request of the judge, an Ohio University law professor filed a friend-of-the-court brief Tuesday that suggested the court had some flexibility in departing from the guidelines.

Douglas Berman, the Ohio University law professor, wrote that rare circumstances are just the type of events that a judge's power of discretion were designed to cover.

William Quigley, a Loyola University New Orleans law professor working on behalf of the activists, said in court papers that the break-in was not the typical case of sabotage involving terrorists. Case law under the Federal Sabotage Act of 1918 is scarce.

"Michael, Greg, and Sister Megan are not the saboteurs, the spies, the bomb making terrorists, or the kind of offenders Congress anticipated when it created the Federal Sabotage Act" in 1918 and when it strengthened it in 1940 and 2001, Quigley wrote.

During the hearing, the judge struggled with how to handle the guidelines.

"At some point, the law has to command respect, and there is a lawful way to change it," Thapar said.

But he also suggested that Rice's past good works should play a role and wasn't sure how to fit those into the guidelines. He called a recommended sentence of 6½ years for Rice "overkill."

Assistant U.S. Attorney Jeffrey Theodore argued that Berman's interpretation was not consistent with federal sentencing guidelines.

Theodore contended the trio's actions were "serious offenses that have caused real harm to the Y-12 National Security Complex."

"They have shown no remorse for their criminal conduct," he said.

Contributing: The Associated Press and WBIR-TV, Knoxville, Tenn. Gang also reports for The Tennessean in Nashville.

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