Although the U.S.-Japan alliance is often labeled as "the cornerstone" of security in the Asia Pacific region, local concerns about the U.S. military presence on the Japanese island of Okinawa have challenged the management of the alliance for decades. The Japanese archipelago serves as the most significant forward-operating platform for the U.S. military in the region; approximately 38,000 military personnel, 43,000 dependents, and 5,000 DOD civilian employees live in Japan. With the United States pledging to rebalance its defense posture towards Asia, the uncertainty surrounding the medium and long-term presence of American forces on Okinawa remains a critical concern for national security decision-makers. Due to the legacy of the U.S. occupation and the island's key strategic location, Okinawa hosts a disproportionate share of the continuing U.S. military presence. About 25% of all facilities used by U.S. Forces Japan and about half of the U.S. military personnel are located in the prefecture, which comprises less than 1% of Japan's total land area. Many observers assert that Tokyo has failed to communicate effectively to Okinawans the necessity and benefits of the alliance. However, Okinawa has received millions of dollars in subsidies from the central government in exchange for the burden of hosting U.S. troops. This year, Tokyo awarded a large amount to Okinawa for the prefecture's economic development plan.

North Korea has been among the most vexing and persistent problems in U.S. foreign policy in the post-Cold War period. The United States has never had formal diplomatic relations with the Democratic People's Republic of Korea (the official name for North Korea). Negotiations over North Korea's nuclear weapons program have consumed the past three U.S. administrations, even as some analysts anticipated a collapse of the isolated authoritarian regime. North Korea has been the recipient of well over $1 billion in U.S. aid and the target of dozens of U.S. sanctions. This report provides background information on the negotiations over North Korea's nuclear weapons program that began in the early 1990s under the Clinton Administration. As U.S. policy toward Pyongyang evolved through the George W. Bush presidency and into the Obama Administration, the negotiations moved from mostly bilateral to the multilateral Six-Party Talks (made up of China, Japan, Russia, North Korea, South Korea, and the United States). Although the negotiations have reached some key agreements that lay out deals for aid and recognition to North Korea in exchange for denuclearization, major problems with implementation have persisted. With talks suspended since 2009, concern about proliferation to other actors has grown. After Kim Jong-il's sudden death in December 2011, the reclusive regime now faces the challenge of transferring dynastic power to his youngest son, Kim Jong-un. Pyongyang had shown signs of reaching out in 2011 after a string of provocative acts in 2010, including an alleged torpedo attack on a South Korean warship that killed 46 South Korean servicemen and an artillery attack on Yeonpyeong Island that killed two South Korean Marines and two civilians. When Kim passed, the United States was reportedly on the verge of announcing an agreement on food aid and Pyongyang had indicated a willingness to freeze some parts of its nuclear program. The Obama Administration, like its predecessors, faces fundamental decisions on how to approach North Korea. To what degree should the United States attempt to isolate the regime diplomatically and financially? Should those efforts be balanced with engagement initiatives that continue to push for steps toward denuclearization, or for better human rights behavior? Should the United States adjust its approach in the post-Kim Jong-il era? Is China a reliable partner in efforts to pressure Pyongyang? Have the North's nuclear tests and alleged torpedo attack demonstrated that regime change is the only way to peaceful resolution? How should the United States consider its alliance relationships with Japan and South Korea as it formulates its North Korea policy? Should the United States continue to offer humanitarian aid? Although the primary focus of U.S. policy toward North Korea is the nuclear weapons program, there are a host of other issues, including Pyongyang's missile program, illicit activities, and poor human rights record. Modest attempts at engaging North Korea, including joint operations to recover U.S. servicemen's remains from the Korean War and some discussion about opening a U.S. liaison office in Pyongyang, remain suspended along with the nuclear negotiations.

Since September 2001, the United States has been concerned with radical Islamist groups in Southeast Asia, particularly those in the Philippines, Indonesia, Malaysia, Thailand, and Singapore that are known to have ties to the Al Qaeda terrorist network. Southeast Asia is a base for past, current, and possibly future Al Qaeda operations. For nearly fifteen years, Al Qaeda has penetrated the region by establishing local cells, training Southeast Asians in its camps in Afghanistan, and by financing and cooperating with indigenous radical Islamist groups. Indonesia and the southern Philippines have been particularly vulnerable to penetration by anti-American Islamic terrorist groups. Members of one indigenous network, Jemaah Islamiyah (JI), with extensive ties to Al Qaeda, are known to have helped two of the September 11 2001 hijackers and have confessed to plotting and carrying out attacks against Western targets. These include the deadliest terrorist attack since September 2001: the 12 October 2002 bombing in Bali, Indonesia, that killed approximately 200 people, mostly Westerners. On 9 September 2004, a suicide bombing attack thought to be the work of JI struck the Australian Embassy in Jakarta, killing 10 and wounding around 200. In October 2005, three suicide bombers exploded bombs within minutes of one another in Bali, killing more than 20 people. These attacks suggest that JI remains capable of carrying out relatively large-scale plots against Western targets, despite the arrest or death of hundreds of JI members, including most of its known leadership. To combat the threat, the Bush Administration has pressed countries in the region to arrest suspected terrorist individuals and organisations, deployed over 1,000 troops to the southern Philippines to advise the Philippine military in their fight against the violent Abu Sayyaf Group, launched a Regional Maritime Security Initiative to enhance security in the Straits of Malacca, increased intelligence sharing operations, restarted military-military relations with Indonesia (including restoring International Military Education and Training [IMET]), and provided or requested from Congress over $1 billion in aid to Indonesia and the Philippines. The responses of countries in the region to both the threat and to the U.S. reaction generally have varied with the intensity of their concerns about the threat to their own stability and domestic politics. In general, Singapore, Malaysia, and the Philippines were quick to crack down on militant groups and share intelligence with the United States and Australia, whereas Indonesia began to do so only after attacks or arrests revealed the severity of the threat to their citizens. That said, many governments view increased American pressure and military presence in their region with ambivalence because of the political sensitivity of the issue with both mainstream Islamic and secular nationalist groups. Indonesia and Malaysia are majority Muslim states while the Philippines and Thailand have sizeable, and historically alienated and separatist-minded, Muslim minorities.