Before dawn on Nov. 7, the highest-ranking officer in Georgia’s military, Giorgi Kalandadze, was on his way to what he thought was a ceremony to welcome home troops from the war in Afghanistan. He was expecting a podium and television cameras at the airport for a flight that was scheduled to land at 5 a.m. Instead, his lawyer says, he was taken to the defense ministry, charged with three counts of physically abusing soldiers, and arrested. He spent the next two days in jail.

Kalandadze was the latest target in a string of attacks on the party and associates of Mikheil Saakashvili, Georgia’s president who rose to power in 2003 in the so-called Rose Revolution. Saakashvili’s government has been a darling of the West, an oasis in a post-Soviet region where tensions with the U.S. have risen under the spreading influence of Russia-aligned dictatorships. In contrast to countries like Armenia, Uzbekistan, and Ukraine, Georgia’s government has openly opposed expanding Russian influence in the region while seeking defense and economic partnerships with the U.S. and Europe. Of all the former Soviet republics, Georgia sent the most troops to the U.S.-led wars in Afghanistan and Iraq. It named the road connecting the national airport to the capital, Tblisi, after George W. Bush. Saakashvili counts Sen. John McCain as a personal friend.

But in his own country, Saakashvili’s luster has begun to wear off—and that could ultimately undermine Georgia’s relationship with the U.S. His opposition has accused of him of employing the same kinds of Soviet-style tactics that he fought against as a young activist, including wire-tapping the phones of the opposition and arresting political activists. On Oct. 1, Saakashvili’s party, the United National Movement, lost parliamentary elections to the DREAM party, a new coalition led and funded by billionaire Bidzina Ivanishvili.

The election at the time was praised as free and fair, but the results are now threatening to rip Georgia’s government in two. After the vote, Saakashvili still controls the military and the national security agencies because he will remain president until the end of 2013. But his chief rival and Georgia’s new prime minister, Ivanishvili, controls the Justice Ministry. This month, the Justice Ministry began targeting senior members of the government and supporters of Saakashvili—including Kalandadze, a Saakashvili appointee—in a wave of arrests that has drawn criticism from the European Union and the State Department.

Senator McCain says the Georgian president has expressed his concerns about the situation in private phone calls. “He’s very concerned about the actions that the new prime minister has taken and the threats to people who served previously,” McCain said in an interview. Saakashvili says he’s worried about the “arrests, threats, and other indications of a lack of respect for the democratic processes.”

In 2008, when McCain was running for the presidency against Obama, Russia invaded the Georgian provinces of Abkhazia and South Ossetia. On the campaign trail, McCain said at the time, “We are all Georgians now,” an echo of Le Monde’s famous editorial saying, “We are all Americans now,” after the attacks of Sept. 11, 2001. Georgia lost the war in 2008 and Russia still occupies Abkhazia and South Ossetia.

In an interview, Irakli Alasania, the new Georgian Defense minister and a member of the DREAM coalition, said, “We are committed to transparency in this case and all cases,” referring to Kalandadze’s arrest. “With all due respect to Senator McCain, I think his assessment is not correct. Justice was selective under Saakashvili.”

Alasania delivered the bad news personally to Kalandadze on the morning of Nov. 7. He says he explained the charges and told him the Justice minister and chief prosecutor in another office would explain more. Alasania says he then told the general, “I will stick with you if you are innocent. There will not be selective and arbitrary justice as it was done during the Saakashvili period. If you are innocent, we will stick with you.”

Now 32, Kalandadze rose quickly through the ranks of the Georgian military. He commanded the brigade in the 2008 war with Russia that suffered the most casualties and he himself was shot in the calf. He is also one of the few Georgian officers to graduate from the U.S. Army's elite Ranger School.

“He was surprised,” Kalandadze’s lawyer, Gogita Gabaidze, told The Daily Beast. “He was taken to the airport under false information. He was surprised. He was deceived. We were all very surprised.”

Kalandadze is being charged with three counts of exceeding his authority as an officer in the Georgian army, according to his lawyer. Gabaidze says the charges are based on the testimony of 19 soldiers who claim Kalandadze physically abused them at times and subjected them to cruel and unusual training, such as singing patriotic songs for hours at a time and grabbing a soldier by his ear. Kalandadze could face up to 17 years in prison if he is found guilty.

Gabaidze says his client is innocent: “I think I am going to win because the only evidence is witness statements and there is no other evidence. The evidence is inconclusive.”

Kalandadze’s sister, Gogola Kalandadze, says she’s less confident. In an interview, she said she thought the trial could go either way. She said her brother’s wife called her the morning of the arrest with the bad news. “When she called her voice was nervous, I heard in her voice that she was afraid,” she said. “I felt like this is like the old days when the KGB would come to your door in the middle of the night.”

Vano Merabishvili, a former prime minister and political ally of Saakashvili, said he, too, has been threatened with prosecution and that he may also face incarceration. “This is a fundamental intolerance of an opposition, of the media, and of local governments,” he said.

Alasania says that’s not true, and says one of the main reasons his party won the election in October is because Georgians no longer trusted the justice system under Saakashvili. Indeed, one of the first moves from the new majority in Georgia’s Parliament was to announce a re-investigation into a series of high-profile espionage cases that accused Georgian citizens of spying for Russia and planting bombs throughout the country in the service of Russia’s military intelligence agency.

Nonetheless, the recent arrests have started to raise concerns in Washington. Sen. Joe Lieberman told The Daily Beast that he was proud of how Saakashvili responded to electoral defeat, but he was worried about how Ivanishvili was responding to electoral victory. “These latest steps are very troubling and I hope the new parliamentary majority will pull back because it’s not what the public wants, it’s not what anyone wants.”

Mark Toner, a spokesman for the State Department, said the U.S. government was following the cases of those who have been detained. “Georgia’s new, democratically elected government has stated clearly its commitment to strengthen rule of law in Georgia,” Toner said. “It is important that these charges be investigated and, if evidence warrants, prosecuted under Georgian law with full respect for due process and the rights of the accused to a fair and impartial trial.”