Sudan, the largest country in Africa was at war. It had been at war for close to two decades, it was a war that was itself a continuation of another 17 years-long war. Adding up to 50 years of sustained conflict, complete with a shifting web of regional alliances. The conflict's current state was a civil war between the northern, Khartoum based government and the southern breakaway provinces. The front lines had been more or less stabilized since the late 90s. Numerous peace initiatives from across the Arab, African and Western worlds had been attempted but none resulted in a successful ceasefire.
The basis of the conflict lay in the differing ideologies and ethnicities of the more Islamic-Arab north and the Christian-East African south. North Sudan's dictator Omar al-Bashir had conducted an Islamist state and as result fostered extreme jihadist sentiment and much western distaste. The United States labelled the country a sponsor of terrorism that once harboured the current leaders of Al-Jihad and Al-Qaida Zawahiri and Atef two of America's most notorious enemies. Relations were briefly calmed during the Clinton administration until an airstrike falsely connected to Al-Qaida struck Sudan killing 85 of the Al Shifa medical plants staff, an attack that severely impacted the country's medical infrastructure and bolstered anti-American sentiment in the country. In turn anti-U.S leadership in the nation rose to a new prominence including Bashir’s second in command Hassan Al-Turabi, he was secretary of the party and speaker of the national assembly and had continued to hold significant sway over Bashir’s dictates.
Sudan President Omar Al-Bashir and key advisor Hassan Al-Turabi
Turabi, vehemently opposed any rapprochement with the west arguing that Sudan should pursue alliances with traditional Arab, Islamic leadership including other so-called terror states. This policy came with heavy repercussions, sanctions were placed on the country and renewed conflict with the south broke out in 2001, to aid themselves in the conflict Sudan made overtures to Al-Jihad, its leader Ayman al-Zawahiri was all too happy to accept, gaining another ally in the Arab world as well as a renewed propaganda and training campaign in the country, and the golden opportunity for war profits.
The country suffered under the regime, reliant on oil exports under heavy sanctions and in an active war, the economy dragged and Sudan continued to stagnate, opposition to the Bashir regime steadily grew. One such area of resistance was the non-Arab minority in the western Darfur region. For a decade the Khartoum government had operated a policy akin to apartheid segregating Arabs from non-Arabs. Arabs were favoured in land disputes, water access and non-Arabs accused the government of oppressing their traditional semi-nomadic lifestyle. In 2002 a low level of conflict simmered in Darfur where rebels consistently attacked police stations and military convoys, though reports were withheld from Khartoum and Bashir. This lasted until a military base was attacked in February 2003 by the Darfur Liberation Group. Bashir outraged, ordered the military to suppress the uprising, but 20 years of war had sapped the army of any reserves and the brass knew that removing troops from the south could destabilise the situation and potentially collapse the front. The rebel groups were also aided by Sudan's neighbours including Chad and Libya. What few regiments could be spared proved unable to even find the rebels, and they occasionally were captured and ransomed back to the government. So instead of the military, Bashir turned to Turabi and the militants.
Turabi utilised his Arab world links to raise and recruit more insurgents to fight the rebels in Darfur, mostly from pan-Arab and Sunni nationalist groups. This recruitment of paramilitary groups grew into the thousands and was integrated into (and took over) the popular defence forces (The PDF) the countries dedicated Islamic militia. The PDF supplanted the national army everywhere, outside of the southern conflict. This new military formation coincided with reports of state-backed terror inside the country committed in both the Darfur and southern region signs of a possible effort to ethnically cleanse the region of non-Arabs.
Popular defence forces (PDF), Islamist militias sent to put down the Darfur uprising
A map of Sudan, including the breakaway southern region outlined in green and the rebellious Darfur region outlined in blue
As the Bush administration outlined global threats, the eyes of the world were turned toward the so-called ‘hermit kingdom’, North Korea and its dear leader Kim Jong-Il. Il had succeeded his father Kim Il-Sung in 1994, needless to say, his reign had gone poorly to date. Throughout the 90s North Korea's economy struggled due to severe mismanagement, thanks to Kim's incompetence in such matters and severe flooding. The country, lacking in arable lands was unable to get sufficient imports into the country resulting in a severe famine that devastated the DPRK. Instead of seeking a solution to the problem Kim, sought to sure up his power base, concentrating on building the nation's military while the country remained dependent on foreign aid for food imports. The military policy made the army the central organizer of all North Korean society.
Former dictator of North Korea Kim il-Sung and his son and current dictator Kim Jong-Il
But Kim Jong Il did strike a different chord than his father internationally, soon rumours of reform made their way to Washington and the Clinton administration began to make serious efforts to normalise relations between the ideologically and geographically disparate nations. The two powers knew that the main issue of conflict between them was North Korea’s 40-year long quest for nuclear weaponry. Both the Soviet Union and the Peoples Republic of China had rejected aiding the North Korean initiative but Kim Il Sung as part of his ‘all-fortressization’
policy doggedly pursued the initiative. But the nuclear process had been a very long one, and though the country claimed to be making strides toward the construction of an atomic bomb, analysts disputed the claim. This did not stop the U.S. from ensuring that the DPRK did not get hold of such a device,
a key aim of its Korean policy going forward. A framework agreement was created in 1994 the 'Agreed Framework between the USA and DPRK',
it focused on replacing North Korea's potentially weaponizable power plants into civilian plants, with the larger focus of normalised policy between the countries. The agreement was troubled from the start, it was both non-binding and voluntary, it was without congressional recognition as a treaty due to opposition detraction. Republicans were especially critical viewing such an agreement as appeasement, Senator McCain called the deal ‘traitorous'. Moves toward reconciliation between North and South Korea were made in 1998 when South Korean president Kim Dae-Jung adopted the sunshine
policy a more liberal and cooperative stance (a policy for which he would win the Nobel peace prize in 2000). Slowly but steadily ground was being gained to bridge the long divide. The Presidency of George Bush threatened to upend this, the state department had created a draft of evidence that accused North Korea of secretly undermining the framework and attempting to construct a nuclear device, the evidence claimed that the DPRK had failed to properly report the amounts of plutonium and that it was testing intercontinental missiles and disguising them as satellite tests. It was clear that the Bush administration wanted a firmer line with the North Koreans, but a lot stood in the administrations' way. The South Korean Government remained committed to the Sunshine policy, convinced that continued dialogue and open negotiations were the best way to reach a détente. Contrary to Bush’s more aggressive tone, he went against his neoconservative advisors on this issue and deferred to the South Koreans after a meeting with Dae-Jung. At home, the Bush administration was tarred as carrying on Clinton's failed policy. Bush publicly responded, the administration used the state of the union address to outline the danger of nuclear proliferation but did not name North Korea. However, the state department accused North Korea of not meeting the Agreed Framework and began to push for a renewed diplomatic effort to ensure North Korea remain permanently denuclearized.
President George Bush visits the demilitarized zone (DMZ) between the Koreas
The renewed diplomatic effort was made in 2003 when North Korea agreed to talks between the United States and North Korea, these talks were supported by South Korea and Japan and resulted in both sides recommitting to the agreed framework, with more funding for converting North Koreas reactors and a further round of nuclear inspection. Allowing both sides to walk away with perceived victories, while eying further talks in the future, aimed at a firmer path toward a lasting relationship. The policy was a rounding of the bases, harsher language and threats that were toned down in favour of staying the course with the option for continued dialogue. 
Another nation pursuing weapons that the Bush administration outlined as a danger to the United States was Libya helmed by its de facto leader Colonel Muammar Gaddafi. Gaddafi had a particularly hostile relationship with the United States, he had throughout his rule financed revolutionary and terror groups across the globe from the IRA to the Japanese Red Army to the Colombian FARCS. The terror had resulted in his nation being bombed by Reagan in 1986 and sanctioned in connection to the bombing of Pan Am Flight 103 in 1988. Libya was becoming increasingly isolated politically, for decades Libya had played the tug of war between the Soviet Union and the United States attracting both bloc's support but the decade since the soviet collapse had not been kind to Libya. Gaddafi had secured the lifting of some sanctions by surrendering two terror connected Libyans but his failure to accept responsibility and apologize left the country with continued economic hardship.
Libyan defacto ruler Colonel Gaddafi
The flamboyant leader aware of Libya’s isolation strained to find support in the west and the United States especially, due to its continued development of chemical and nuclear weaponry. Just like North Korea the colonel also held a decades-long ambition to acquire such powerful weaponry for the official purpose of countering Israel’s nuclear program. The programme had been aided by the Soviet Union and the black market in its development but unfortunately for Gaddafi, his goals were hampered by the economic sanctions and the fall of the Soviet Union long delaying the project's progress. The Libyans, aware of their isolation even approached President Clinton with a blunt offer to end its nuclear weapons program in return for lifting sanctions but such efforts stalled over Gaddafi’s continued refusal to apologise for terror connections. To many including scientists, analysts and spies Libya’s nuclear programme was a pipe dream, but the country did still hold a sizable illicit chemical weapons programme still a potential threat. The regime faced a conundrum, could it make a deal with the west, turn back decades of policy in return for reintegration with the international community, it was a possibility but for the moment the west had little to offer. Neither Bush nor Blair would drop the demands for apologies and compensation and gave no firm commitments to drop sanctions even if such efforts were made, let alone encourage investment in the country. Besides, Gaddafi had new estimates on the countries programme including one made by his son Saif that the programme was only a mere 5 years away from completion, what was to be lost? Surely achieving such a monumental goal would force the west to meet Libya at the negotiating table, seriously this time. The decision was made, and over the months of 2002 and 2003 cargo ships snuck into the country, using ties to the Pakistani nuclear programme and the “nuclear black market”, containers packed with centrifuge parts were taken ashore in Tobruk, finally after a 30-year long teething period, the Gaddafi regime got serious on its nuclear programme. 
Gadaffi attending a military parade in his honour
Perhaps the reason the Bush administration proved unable to spot the uptick in Libya’s march toward WMDs was the administration's fixture on other nations. Of course, Iraq made the biggest headlines, and Saddam was publicly identified as the greatest threat to the United States and special attention was being paid to Iraq’s possible weapon programme following his state of the union speech, this was followed by North Korea who’s bombastic threats never failed to grab the world’s attention but quietly the administration shifted away from another Clinton era foreign policy, regarding the Islamic Republic of Iran. For decades the United States and Iran had fared off in a virtual proxy conflict but starting in 1997 with the election of a moderate Iranian President Mohammad Khatami, the Clinton administration began engaging in a dialogue and a slow easing of sanctions with the nation. Attempts at a full dialogue failed between the two, over Israeli policy, which the Ayatollah was unwilling to compromise over, however, progress was made, Secretary Albright acknowledged the US role in the 1953 Iranian coup listing the Shah as a repressive ruler, and the USA lifted sanctions on non-oil related products. Bush, in contrast, held a tougher stance, he refused to roll back sanctions and ramped up the tough talk. They blamed Iran for spoiling the Arab Israeli peace talks by funding Palestinian and Lebanese anti-Israeli groups and expressed the utmost concern at the Iranian government’s possible nuclear capabilities.
President of Iran Mohammad Khatami and Supreme Leader Ayatollah Khamenei
Iranian policy was again split between the Cheney/Rumsfeld neo-conservative idealists and the Powell led pragmatists. Bush aired on the side of the hardliners this time, who perceived the Iranian regime as teetering, and believed it to be just as vulnerable to a potential collapse as Saddam’s Iraq. Thus any attempt at normalizing the Islamic theocratic leadership would be to the detriment of the ‘democratic’ forces inside Iran. The hardliners were successful in separating Iran from the US’s foreign policy dialogue, this included Afghanistan where, despite the Shia majority Iran (who could have proved an important ally as an opponent to the Sunni dominated Taliban), Washington sought to cut out Iran and Iranian influence from the Northern Alliance against the wishes of Massoud. The Bush administration's policy came round to maintaining the status quo of harsh relations and ignoring the country otherwise.
Iran, in turn, replicated the foreign policy, postponing dialogue, so too did they postpone a shift in their nuclear policy, where President Khatami who had been prepared to negotiate instead continued to conceal the country’s nuclear facilities, he gave away no hints as to the countries plans. Iran despite being a signee to the non-proliferation treaty continued to improve its potentially weaponizable capabilities, by 2003 the technological extent of its programme surpassed what any western intelligence predicted, especially as the United States had done everything to slow down any kind of nuclear tech inside Iran. However, such secrecy could not be kept forever, and through 2003 Iranian opposition groups began to leak information about the programme. These leaks, however, went unheeded, the United States doubted such claims since the data was usually brought forward by Iraqi backed anti-Iranian groups and was viewed as an attempt to shift eyes away from Bagdad and toward Tehran. Khatami’s reformist rule struggled in the face of the Bush administration but it struggled forward regardless, unlike Libya there was no rush to build a bomb and the ultimate goal remained to force the US to negotiate with them, it just so happened that this specific road would be much longer than the one Khatami hoped for. 
Irans reform focused President Mohammad Khatami "The man with the chocolate robes"
 Sudan and Bashir maintain an anti-American stance extending the conflict in South Sudan and leading to a bloodier conflict in Darfur. As well as a still growing Islamist faction.
 I believe that the Bush doctrine convinced North Korea that the United States might invade and that China wouldn’t support them if they did so. ITTL neither of those are true so there is no real rush toward acquiring a nuclear weapon.
 Gaddafi was clearly a political opportunist who was willing to give Blair and Bush a significant political win when they needed it most in return for Libya’s normalisation. ITTL no such deal is on the horizon no one even believes Libya’s programme to be legitimate. So, Gaddafi follows his son's terrible advice and doubles down.
 ITTL there is no Axis of Evil speech, the event that triggered all the alarm bells in Tehran and convinced a lot of Iranians that the United States was aiming for regime change there too. Here US Iranian relations are hostile but not disastrous.