The visit was aimed at bolstering Georgia’s ambitions to join NATO, which are supported loudly by the US but appear overwhelmingly opposed across the rest of the alliance. The elephant in the room was the 2008 Russo-Georgian War.

In that brief war, Georgia attacked Russian forces in the secessionist enclave of South Ossetia. The result was massive Russian retaliation, which destroyed much of Georgia’s military and saw both South Ossetia and Abkhazia declaring formal independence from Georgia.

The US has refused to recognize the new republics, and even today Obama reiterated his support for Georgia’s “territorial integrity,” including reclaiming both of those territories. Saakashvili has vowed to reclaim them by any means necessary, but both have reached security deals with Russia which make such a reunification virtually impossible.

The security arrangements also stand in the way of Georgia’s NATO ambitions, as the alliance is never going to agree to admit the nation given the current situation on the ground. Both sides were careful not to mention the war in today’s talks, but it will cast a big shadow over all dealings with the Georgians going forward.

According to Saakashvili, the bombing was “payback” for the brief Russo-Georgian War of 2008, and that he had recently told Russian Prime Minister Vladimir Putin that he would face “payback for his country for supporting separatists.”

The comments came in the wake of Putin’s own statement that Chechnya, which was initially assumed to be the source of the attack, had nothing to do with it. Putin did not describe who was responsible, however.

Saakashvili’s comments, though presumably not a claim of responsibility, are likely to spark another round of anti-Georgian sentiments in Russia. Tensions between the two sides have flamed up repeatedly since the war, and have regularly led to attacks on Georgian immigrants living in Russia.

The move sparked outrage from neighboring Georgia, which has designs on reannexing Abkhazia after the 2008 declaration of independence. Russia has set up a military base in Abkhazia and has signed a pact agreeing to defend them from a future Georgian attack.

Yet US State Department spokesman Philip Crowley insists the deployment is nothing new, and says it was America’s understanding that the S-300 had been in Abkhazia for the past two years, since the end of the brief Russo-Georgian War in August 2008.

Georgia’s Deputy Prime Minister said the deployment posed a threat to the whole of Eastern Europe, including a number of NATO members. The claim is unlikely to be considered very credible, however, as the S-300 has only defensive uses.

Georgian President Mikhail Saakashvili, for his part, vowed to continue his “struggle for liberation,” which is the official euphemism for rolling back the secessions of South Ossetia and Abkhazia and reintegrating them into the Georgian nation-state.

Temur Iakobashvili, his government’s Minister for Reintegration, touted the Georgian government’s achievement of managing to avoid international recognition for either of the enclaves, and said his government’s next goal was to get the rest of the world to declare them “occupied territories,” on the grounds that Russian soldiers are backing up the republics’ claims to independence and preventing Georgia’s military from reannexing the regions.

Beyond Russia, the secession of the two enclaves is not generally recognized, but in the wake of the UN court’s opinion on the legality of Kosovo’s secession, South Ossetia and Abkhazia too may have gained an air of legitimacy, albeit one clouded by the diplomatic row between Russia and NATO. The United States has pledged to use its position in the United Nations to prevent the two enclaves from ever being recognized internationally.

Of course there is no real mystery surrounding the war at this point, as the European Union has issued reports in excruciating detail of the early hours, in which Georgian troops attacked the South Ossetian city of Tshkinvali and Russia responded by destroying much of Georgia’s military.

But in the wake of the war the redrawn borders, or rather the lack of official recognition for borders which had for all intents and purposes been redrawn years prior, remains a sore point. Two breakaway republics, South Ossetia and Abkhazia, had been trying to secede from Georgia for years, and Russia formally recognized this secession in the wake of the August 2008 war. The US has refused to acknowledge the new nations, though they had both been de facto independent for years prior to the war.

And it is these two republics that remain at issue, and are the source of Clinton’s claim of “occupation.” Georgian President Saakashvili had promised to use “any means necessary” to reconquer the two enclaves, and with the US pumping military aid into the Georgian government one of the first acts of the newly elected Republics was to ask Russia to sign defense pacts, which they promptly did.

The deals cemented a Russian military presence in both enclaves for the long term, but also provided both republics with a means of survival against a near term threat of invasion. Clinton’s condemnation is in keeping with the US policy not to recognize the new nations’ rights, though in the long run it appears Georgia has no chance of re-obtaining them through military means, and the policy will only serve to be a sore spot in future relations.

Following up on reports from the weekend, the Pentagon is confirming some $50 million in aid to be distributed more or less equally among Georgia, Croatia, Hungary, Latvia, Lithuania, and Estonia.

The $50 million is just the tip of the iceberg, and the overall program could cost upward of $350 million. It will include funding for both equipment for the nations, whose overall commitment amounts to just over 1.2% of the overall military force in Afghanistan.

Though the Pentagon insisted that the funding did not amount to “bribery,” they conceded that it was in part an incentive for the nations to keep literally scores of troops in the nation.

It keeps a large number of “partners” involved in the war, but does little for NATO efforts to increase the number of troops in the nation, as Canada and the Netherlands, both poised to leave, each contribute far more troops than all of these nations combined.

Enter the Republic of Georgia, the nation that eagerly took part in the US occupation of Iraq. They had to abandon that war in August 2008 to fight a brief war with Russia. While that war does not appear to have exhausted the Georgian government’s willingness to fight, it did destroy their military nearly in its entirety.

This is nothing the Pentagon believes it cannot solve with increased military aid however, and they have informed Congres that they intend to build the military capabilities of Georgia and several other minor powers in eastern Europe with an eye toward conducting “operations alongside US forces in Afghanistan.”

Yet nothing comes without a cost, and while the financial cost will be borne by the US taxpayers, the artificial increases in the sizes of these militaries could have serious ramifications on those nations and the surrounding area. Nowhere is this more apparent than in Georgia, where the last US-built military attempted to seize South Ossetia militarily, sparking the aforementioned war with Russia. Georgian President Saakashvili remains keen to reclaim South Ossetia and Abkhazia by any means possible, and even if in the near-term that military is going to be used in Afghanistan, its long-term ambitions remain with the now-independent enclaves to their north.

Also as expected the report faulted the Russian government for retaliation “far beyond the reasonable limits of defense” when it essentially destroyed the entire Georgian military in response to the incident.

Both Georgia and Russia lauded the report, saying it vindicated their respective positions with regard to the war. A spokeswoman for Russian President Dmitry Medvedev said the commission’s conclusion was what “Russia has clearly and repeatedly stated.”

Georgia however told a different story, with its official statement claiming the EU had proven that the war was all Russia’s fault and that any Democratic nation would have launched the same attack as Georgia did in the face of “invasion.” The EU commission responded to the claim by noting that the group was never able to substantiate claims of a Russian invasion before the shelling.

In an effort to make the report more palatable to the eastern EU member states which have an axe to grind against Russia, the report will also accuse Russia of “exploiting” the conflict and will criticize them for distributing Russian passports to residents of the separatist enclaves of South Ossetia and Abkhazia, which declared independence after the conflict.

Georgia has officially reacted with outrage at every report regarding the war, insisting that Russia actually started it. But even former Georgian officials acknowledge that President Mikheil Saakashvili was “itching” to do battle over South Ossetia, and test the high-tech military which was largely destroyed in the brief conflict.

President Saakashvili has vowed to reclaim the enclaves as parts of Georgia proper, and has US support in ensuring they will never be recognized as independent republics, though in practice both have been outside Georgian control for quite some time.

Following the pact, the Russian Coast Guard has warned that it will not allow the naval blockade to continue, and says it will detain any Georgian military ships which attempt to enter Abkhaz waters.

Georgia condemned both moves, saying the military pact proved that Russia was “barbaric” and that the coast guard’s comments proved that the Russian Coast Guard are pirates under international law.

Long enjoying de facto independence from Georgia, Abkhazia and South Ossetia declared formal independence following the August 2008 Russo-Georgian War. Georgia has not recognized the independence of either and has promised to use any means necessary to reclaim control over them.