SPLA-led offensive against the Sudanese government
Operation Thunderbolt (9 March – late April 1997) was the codename for a military offensive by the South Sudanese SPLA rebel group and its allies during the Second Sudanese Civil War. The operation aimed at conquering several towns in Western and Central Equatoria, most importantly Yei, which served as strongholds for the Sudanese Armed Forces (SAF) and helped the Sudanese government to supply its allies, the Ugandan insurgents of the WNBF and UNRF (II) based in Zaire. These pro-Sudanese forces were defeated and driven from Zaire by the SPLA and its allies, namely Uganda and the AFDL, in the course of the First Congo War, thus allowing the SPLA to launch Operation Thunderbolt from the Zairian side of the border. Covertly supported by expeditionary forces from Uganda, Ethiopia, and Eritrea, the SPLA's offensive was a major success, with several SAF garrison towns falling to the South Sudanese rebels in a matter of days. Yei was encircled and put under siege on 11 March 1997. At the same time, a large group of WNBF fighters as well as SAF, FAZ, and ex-Rwandan Armed Forces soldiers was trying to escape from Zaire to Yei. The column was ambushed and destroyed by the SPLA, allowing it to capture Yei shortly afterward. Following this victory, the South Sudanese rebels continued their offensive until late April, capturing several other towns in Equatoria and preparing further anti-government campaigns.
The success of Operation Thunderbolt significantly strengthened the SPLA in Western Equatoria, and weakened the Sudanese government's control over its southern territories. The South Sudanese rebels were thus able to expand their operations, and raised global awareness for their cause. Furthermore, the WNBF and UNRF (II) suffered heavy losses during the offensive. Taken together with their defeats in the First Congo War, they were permanently weakened, and in case of the WNBF, effectively defeated as active fighting forces.
Background.
Civil war in Sudan.
Following its independence in 1956, Sudan had suffered from numerous internal conflicts over political, ethnic, and religious issues. In 1983, revolutionaries and separatists from the country's mostly Christian-Animistic south banded together and launched an insurgency against the government which was traditionally dominated by Muslim elites from the north. The rebels organized themselves as the "Sudan People's Liberation Army" (SPLA) under the leadership of John Garang, and the insurgency eventually escalated into a full civil war that also affected Sudan's east and west. Negotiations between the government and the SPLA almost resulted in a peaceful solution of the conflict, but ended after the 1989 coup d'état which brought the National Islamic Front (NIF) under Omar al-Bashir to power. The new regime was militantly opposed to any compromise, and was determined to completely crush the SPLA and all other opposition groups. An escalation of violence followed.
By 1991, the civil war had developed into a "network of internal wars" between the government and a multitude of rebel groups with widely diverging backgrounds and aims. Though the SPLA had grown in power and seized control of large parts of southern Sudan, it also suffered from internal disputes and had never enjoyed the support of the entire southern population. Many in the south had sided with the government or rebel groups that were opposed to the SPLA.
The region of Equatoria, including the important town of Yei, was strongly contested between the SPLA and the SAF for several years. The SAF would control the towns, whereas the rebels held much of the countryside. In the 1990s first half, however, the government managed to regain some ground in the area, retaking several locations from the rebels. At the time, the South Sudanese separatists were weakened by internal divisions and the collapse of the People's Democratic Republic of Ethiopia, their most important foreign ally. By 1994, the SPLA main faction under Garang's leadership was on the verge of complete defeat. Parts of the rebel movement had split off, and some of these splinter groups (such as SSIM/A) had even allied themselves with the government. The SPLA did however manage to recover and regain some strength in the Equatoria area. This was also thanks to the resumption of support by Ethiopia in 1995. Though the country's old, pro-SPLA leadership had been overthrown during the Ethiopian Civil War, Ethiopia's new government under Meles Zenawi was undermined by Sudan, and consequently decided to aid the South Sudanese separatists. Bashir's regime also alienated its former ally Eritrea, so that the latter began to assist the SPLA from 1994.
The Ugandan-Sudanese conflict.
The Sudanese government suspected that the survival of the South Sudanese rebels was dependent on support by the neighboring country of Uganda. This belief was not based on hard facts, but an assumed personal connection between SPLA leader John Garang and Ugandan President Yoweri Museveni. In truth, the two barely knew each other, and Museveni had intended to stay neutral in the Sudanese conflict. He repeatedly attempted to convince the Sudanese government of his non-involvement with the SPLA, and followed a policy of appeasement. This course yielded no results. The anti-Western, Islamist National Islamic Front government of Sudan regarded the Leftist, pro-United States government under Museveni as a natural enemy and supporter of the South Sudanese separatists. Furthermore, the Sudanese leadership intended to islamize the Great Lakes region, and in the context of this plan, mostly Christian "Uganda stood in the way".
In an effort to topple Museveni's government, Sudan thus supported and even organized several Ugandan insurgent groups from 1986, though the extent to which these rebels actually followed Sudanese orders varied greatly. By 1996, the most important pro-Sudanese Ugandan rebel groups were the WNBF, the UNRF (II) (a WNBF splinter faction), the ADF, and the LRA/LSA. Though these groups were not strong enough to actually threaten the Ugandan government, they could undermine its legitimacy by attacking the Ugandan population and further damage the country's struggling economy. They were generally based in southern Sudan or eastern Zaire (present-day DR Congo), whose dictator Mobutu Sese Seko tolerated their presence out of enmity toward Museveni. The Ugandan President responded to the Sudanese and Zairean support for these rebel groups by ending his neutrality in 1993. Uganda started to aid, and then coordinate with the SPLA in their common struggle against Sudan, the Ugandan insurgents, and Zaire. Furthermore, the conflict along the Sudanese-Ugandan-Zairean border intensified, as not just the various rebel factions but even the Sudanese and Ugandan militaries launched cross-border raids and bombardments.
Prelude.
This volatile situation further escalated upon the outbreak of the First Congo War in 1996, as an alliance of rebel groups and states led by Rwanda invaded Zaire to topple Mobutu. Uganda joined this coalition, realizing that the war was an opportunity to eliminate Zaire as haven for Ugandan insurgents. As result, the Uganda People's Defence Force (UPDF) invaded northeastern Zaire, and helped the SPLA and the native Alliance of Democratic Forces for the Liberation of Congo (ADFL) to clear the region of the Zairian Armed Forces (FAZ) and other pro-Sudanese forces. Sudan attempted to aid its allies, but the FAZ was in a catastrophic condition and the Ugandan insurgents demotivated. Both were easily routed by the UPDF and its allies, and surrendered, deserted or fled "en masse" into southern Sudan.
With the pro-Sudanese forces in Zaire routed, the SPLA and its supporters occupied northeastern Zaire. The SPLA was thus in the position to launch offensive operations into Sudan from the Zairian side of the border. Two offensives were planned: "Operation Thunderbolt" which would take place west of the Nile, and "Operation Jungle Storm" east of the Nile. The South Sudanese rebels amassed a force of about 12,000 fighters, including tanks and artillery, for Operation Thunderbolt. Salva Kiir Mayardit was appointed overall commander of the SPLA troops involved in the offensive. Another important rebel commander during Operation Thunderbolt was James Hoth Mai.
The SPLA enjoyed strong support by foreign states, namely Uganda, Ethiopia, and Eritrea, during the preparation and execution of Operation Thunderbolt. Each of these countries had its own goals which it hoped to achieve by aiding the SPLA in capturing Western and Central Equatoria. For Uganda, Operation Thunderbolt's main aim was to capture the entire border to block the SAF from advancing into Zaire to help its allies there. By helping the SPLA, Ethiopia intended to pressure the Sudanese government into ending its support for anti-Ethiopian militants. Eritrea hoped that its involvement in the conflict would weaken its rival Sudan, and reduce the influence of its other rival, Ethiopia, in southern Sudan. The foreign support for the SPLA during Operation Thunderbolt took several forms. First of all, the rebels were trained, provided with intelligence, and supplied with equipment by the UPDF, the Eritrean Army and the Ethiopian Army. Furthermore, many of the tanks and artillery pieces that took part in the operation were operated by crews belonging to the Ugandan, Eritrean, and Ethiopian militaries. Unidentified Ethiopian military officers directly commanded parts of the anti-Sudanese operation. President Museveni even ordered the UPDF to train at Monodo for a potential attack on the Sudanese border town of Kaya.
The offensive.
The SPLA began the offensive amid the dry season on 9 March, attacking the Kaya and the road between Yei and Juba. The assault on Kaya was preceded by an artillery bombardement, and spearheaded by the Uganda People's Defence Force with tanks, howitzers, mortars, and machine guns. The Ugandan forces were under the overall command of Salim Saleh, with Katumba Wamala as operational commander. A task force of UPDF tanks led by Hannington Kyazze crossed a nearby river, and attacked Kaya from the rear. The SAF had previously realized that the SPLA was preparing an offensive, but the rebels managed to capture Kaya on the first day of the attack nonetheless, while the UPDF seized the strategically important nearby Koboko Mountain. Much heavy equipment fell to the UPDF at Kaya, while the town's remaining SAF soldiers retreated to Yei. The UPDF consequently destroyed a SAF artillery unit at Poki Hill near Kaya. On 10 March, the SPLA and UPDF captured Bazi and Gumuni, while the Sudanese and Ugandan militaries reportedly exchanged artillery fire across their common border.
The SPLA was thus able to encircle the SAF in a "massive pincer movement", and cut off the "big" garrison at Yei from Juba on 11 March. This rapid advance was "facilitated primarily by an Ethiopian tank unit", and UPDF tanks also played a major role in clearing the way for the South Sudanese rebels. Attempts by the Sudanese Air Force to supply Yei by air failed, as the air drops were captured by the rebels. In response to the rapid SPLA advances, the Sudanese government ordered the WNBF and UNRF (II) to aid the SAF in rearguard actions; this did little to stop the South Sudanese rebels. Instead, the Ugandan insurgents suffered heavy losses. Their worst defeat came amid the siege of Yei. Over 4,000 stragglers, including women and children, had fled Zaire, crossed the border at Morobo County, and advanced toward Yei. This column included WNBF forces under Juma Oris, as well as a smaller number of FAZ, SAF, and Ex-FAR soldiers. They hoped to find refuge at Yei, and did not know of the town's encirclement by the SPLA. 
Instead of relieving Yei's garrison, the column was ambushed by the SPLA about halfway between Morobo and Yei, and suffered 3,000 casualties: 2,000 killed and 1,000 captured. The survivors were routed and fled in disarray to Juba. The column's leaders were mostly killed, wounded or captured: WNBF commander Juma Oris was badly wounded though escaped, while Ex-FAR Captain Jean-Marie Magabo was captured. Following this defeat, Yei's garrison surrendered on 12 or 13 March, though many of its fighters attempted to flee into the bush. They left behind much materiel, including at least nine 122mm howitzers, one 37mm anti-aircraft gun, and five Chinese-made T-59 tanks. Several WNBF fighters, including the militia's deputy commander Abdulatif Tiyua, were also captured in the town. The Sudanese government responded by ordering 2,000 SAF soldiers who were retreating toward Juba to instead march on Yei, officially to aid the besieged garrison, although the government knew that the town had already fallen. This counter-attack failed, and 1,000 SAF soldiers were captured or surrendered, while the rest were killed or scattered by the rebels.
The SPLA further advanced after its success at Yei, capturing the garrison towns of Morobo (12