Though the military deployment in Japan was historically about posing a threat in the Pacific to the Soviet Union, Gates insisted that the troops are there to “keep China’s rising power in check” and to target North Korea, which one would figure was more the reason the troops in South Korea are there.

Still, Gates predicted that without the troops in Japan, China would “act more aggressively” against US interests, and war games in the region would be “harder.” Though Japan and China are traditionally rivals, the growing Japanese antipathy over the massive US military presence on Okinawa seems like it’s going to need more justification than that.

In the end, the claims of grave threats that warrant such a presence ring extremely hollow. China is an ally, and economic ties ensure that far more than the threat of US attacks. North Korea, on the other hand, is teetering on the brink of collapse, with South Korea openly talking about annexation. Neither seems a major “threat” to either the US or Japan.

But Secretary of Defense Robert Gates insisted that the US would be taking a more conciliatory tack, at least sort of. Gates expressed understanding of the “complex matter” and said the US would show patience while the Japanese government silenced popular opposition to its base amongst Okinawans.

When Japan’s Democratic Party (DPJ) came to power they were openly discussing kicking the US military off the island entirely, but US demands for massive cash payments for even a minor reduction of the amount of the island they occupy and angry rebukes quickly stifled the effort.

The US currently has about 47,000 troops in Japan, and appears determined to keep its presence more or less forever. The land usage and noise problems related to the deployment is a constant complaint for Okinawans, but the US stance has been consistently to ignore it.

The test was the first of the Obama Administration, and will likely spark further questions about the president’s much heralded “commitment” to disarmament. Yet in Japan, and particularly in the cities of Hiroshima and Nagasaki, the idea of continued nuclear weapons testing, even in limited forms, is of far more serious concern.

“The experiment is a reversal from an international trend for a world without nuclear weapons. I feel extreme regret,” said Nagasaki’s mayor, Taue Tomihisa. Officials with the Nagasaki city government intend to send a formal letter of protest. Hiroshima’s mayor, Akiba Tadatoshi, is said to have already submitted such a letter.

Japanese officials also expressed anger at US Ambassador John Roos attending a memorial ceremony in Nagasaki for the 65th anniversary of the nuclear attack, just 11 days after the test took place. US officials say the test is “in line with Washington’s stance to maintain nuclear deterrence.”

Hatoyama’s party came to office on the back of campaign pledges to pursue an independent foreign policy and calls to renegotiate cushy US base deals made by the long-standing ruling party, but in the end US refusal to negotiate and Hatoyama’s inability to organize convincing resistence ended any hope of him accomplishing anything.

The resignation was likely under heavy political pressure, as has popularity flounders and his party struggles to compete in the upcoming election. Hatoyama’s political strategist is said to have resigned as well.

It is unclear so far who will replace the prime minister, but with his approval rating having gone from 70% to the mid teens in just eight months, anyone will likely be welcomed as an alternative.

Hatoyama’s Democratic Party of Japan (DPJ) took power in late August after campaigning primarily on opposition to the ruling party’s support of keeping US military presence on the southern island.

But even after the DPJ was swept to power in the biggest power change in Japan since World War 2, the US made it clear that they would not negotiate with the new government, but would retain the base.

The split over the base led to some diplomatic tensions, but Hatoyama finally backed down and has allowed the base to remain. Okinawa Governor Hirokazu Nakaima was critical of the decision, saying was a betrayal of Hatoyama’s campaign pledge.

The Okinawans are overwhelmingly opposed to the US bases, which take up a significant portion of the crowded island. The DPJ initially threatened to oust the US from the island entirely, though it is clear at this point that this was an empty threat.

Not long after taking power last year, the Democratic Party of Japan revealed that they had found documents proving that their predecessors had signed secret deals with the United States as early as 1960 regarding nuclear weapons. The announcement came with the pledge of a full report.

Rumors of the deal, a flagrant violation of Japan’s non-nuclear stance since it was attacked with nuclear weapons in 1945, have been long-standing, but the LDP governments had repeatedly denied that any such deal existed. It is unclear what, if any, legal ramifications those who were in power at the time might face, but the current government is likely to gain big from uncovering it.

The US State Department downplayed the possibility that it might have any impact on US-Japan relations, saying they had lived up to their end of the treaties. This does appear to be the case, though they had to know at the time that the treaties were illegal under Japanese law. The Pentagon, for its part, refused to comment at all, saying that they don’t discuss specific nuclear weapons movements.

Rather, according to Iran’s Foreign Ministry, they have taken the advice of the IAEA and are now looking for some new third parties with which to reach a comparable enrichment deal.

The initial deal stalled over Iranian concerns of the use of France as a partner in the deal, as France previously reneged on a nuclear deal with Iran and there was concern that, if Iran shipped a large portion of its uranium stockpile abroad, it would simply disappear into France, with nary a trace but some harsh rhetoric from the Sarkozy government.

Western officials have not commented yet on Iran’s latest tack, but they will likely take a dim view of some other nuclear power doing the enrichment after spending months trying to convince the world that the “draft” agreement they submitted to the IAEA was an all-or-nothing proposition, which could never be revised or even clarified publicly.

Japan is seen as a likely partner in such an effort, however. The Japanese government is keen to see the situation resolved amicably, as they stand to lose greatly from rising anti-Iran sanctions. Iranian Parliament speaker Ali Larijani visited Japan late last month, and reportedly came out of it with an early proposal for Japan to enrich uranium for Iran’s medical research reactor.

China in particular has a significant trading relationship with Iran, and has opposed international sanctions repeatedly. Key petrochemical companies in Britain and France could also be protected by this exemption as well, but China is the most controversial.

Particularly angered are key US allies South Korea and Japan, who would stand to lose considerable trading relationships with Iran to the sanctions and would not get the special exemption China would.

Congress is keen on pushing forward the sanctions, but the exemption will likely be a tough sell. Senators note that President Obama would under the existing bill already have the power to subjectively enforce the sanctions at any rate, and would likely shy away from taking the blame for watering them down.

The DPJ instantly started a clash with the US over deals made by the previous government on US military bases. The US, unused to being questioned on its policy in Japan, has flat out refused to negotiate going forward.

But while it is unclear how much the DPJ can really do about the base deals, it is proving increasingly reluctant to accept the “kindness budget,” a euphemism for the annual outlay (currently at about $2 billion) of Japanese government funds to subsidize the US forces in Okinawa.

With US bases eating up a good chunk of Okinawa and the US demanding $6 billion in “relocation costs” from Japan to move 8,000 of those troops to Guam, the DPJ is increasingly seeing these expenses, particularly during the economic crisis, as something they can do without.

Okinawans are irked by the amount of land the bases take up, and the excessive opulence of the bases, which come complete with their own golf courses on the crowded island. The US State Department insists that the bases are not any different than anywhere else in the world, and that even with the Japanese subsidies the US still pays some $3.9 billion a year to keep the forces there.

Japan’s recently elected government says it has found documents that prove that the nation indeed signed a secret 1960 pact with the United States allowing it to transport nuclear weapons through Japanese territory.

The Liberal Democratic Party (LDP), which had a virtually unbroken hold on power for the last half a century, had repeatedly denied that the long-rumored pact existed, but just days after taking office the new Democratic Party of Japan (DPJ) government launched a probe into it.

Since the announcement from the Foreign Ministry, a former vice foreign minister from the LDP has come out anonymously to confirm that he saw the minutes from the 1960 meetings related to the pact when he was in office.

The government says the probe is still ungoing, but the final report won’t be released until January. When that happens, it may further strain relations between the US and Japan’s new government, which has suggested it wouldn’t let a nuclear pact stand.