Here is a good read about the future of the US-Japan alliance that encompasses more than just the Okinawa base issue:

That pledge notwithstanding, for decades there have been rumors of a secret “don’t ask, don’t tell” arrangement between Japan and the U.S. that allowed the U.S. to keep nuclear weapons on ships and aircraft that stopped in Japan or transited its waters.

Previous Japanese governments denied this deal existed, and it became moot in 1991 when then-President George H.W. Bush ordered the removal of all tactical nuclear weapons from deployed U.S. ships and aircraft.

Nonetheless ― and here’s the rub ― the U.S. still follows a strict “neither confirm nor deny” policy in discussing the presence of U.S. nuclear weapons anywhere to avoid precedents that could limit its flexibility or threaten operational security during periods of crisis or conflict or compromise nuclear storage facilities on U.S. territory.

As part of its “transparent government campaign,” the DPJ pledged that it would uncover the truth behind the allegations if it won the August parliamentary elections.

After taking office, Foreign Minister Okada Katsuya said his office would launch an inquiry and “We will reveal everything we find.” Fine; then what? Let’s say that the Hatoyama government comes up with “proof” that such a deal existed. What happens next?

Is the Hatoyama government then prepared to announce “case closed” and move on or will it feel compelled to take measures to ensure that this could never happen again ― a move that would force Washington to choose between maintaining its “neither confirm nor deny” policy or maintaining the alliance?

That might seem like a simple choice to the Japanese but it is not so easy for Washington, which has to always keep one eye on precedents and how this would affect operations and alliances elsewhere.  [Korea Times]

I continue to maintain that Hatoyama is the second coming of Roh Moo-hyun.