Uganda gained independence from the UK in 1962, and saw five years of multiparty democracy under President Milton Obote before his regime began sliding towards violent dictatorship. Obote was ousted in 1971 by a non-commissioned army officer, Idi Amin Dada, whose coup was initially welcomed with widespread enthusiasm.

Amin, however, quickly dissolved parliament and altered the constitution, granting himself absolute power and eliminating all opposition. His eight-year rule was brutal. It is estimated that hundreds of thousands of people were killed during his regime, and he particularly targeted the Acholi people of northern Uganda, partly because of their support for his predecessor but also because they traditionally composed the bulk of the army, and thus posed a potential threat to his reign. Amin's government devastated the country and its developing economy, in part by expelling all Asians from Uganda and thus undermining a growing merchant class.

A victim of his own excesses, Idi Amin was overthrown in 1979 by a Tanzanian-backed rebellion that included current President Yoweri Museveni. However, Obote was able to return to power through rigged elections in 1980, prompting Museveni to launch a guerrilla war in 1981.

Obote's new regime committed massive human rights abuses in an effort to crush Museveni's continued insurgency. As tensions built, Obote was being overthrown in 1985 by a group of ethnic Acholi people led by General Tito Okello. Exhausted by the war and internal divisions, the new Okello regime entered into negotiations with Museveni's rebel group, the National Resistance Movement (NRM). Museveni's National Resistance Army, however, continued its push to Kampala, took the capital in 1986, and installed a "no-party democracy," which allowed individuals, but not political parties, to run in elections.

Museveni is credited with leading Uganda's emergence from the violent and abusive times of Amin and Obote, and with laying the groundwork for the development of one of Africa's more successful economies. But Uganda's security deteriorated in the wake of the 1994 Rwandan genocide, when the perpetrators fled to what was then Zaire (now the Democratic Republic of the Congo) and attempted to regroup with the tacit support of the Mobutu government. In 1996 Uganda joined Rwanda in support of a Congolese rebellion led by Laurent-Désiré Kabila and the Alliance of the Democratic Forces for the Liberation of Congo (AFDL). Together, the AFDL and Rwandan and Ugandan militaries moved into and across the Congo, reaching Kinshasa in May 1997.

A year later and as Laurent-Désiré Kabila began to break away from his former allies, Uganda joined Rwanda in support of a new Congolese rebellion, the Congolese Rally for Democracy, and soon thereafter sponsored its own Congolese rebel group, the Movement for the Liberation of the Congo, led by Jean-Pierre Bemba. What unfolded in eastern Congo was a major war involving six state militaries and a broad array of non-state actors and rebel groups and also spawned the exploitation of Congolese natural resources by all of these forces, and military battles between Uganda and Rwanda for control of the town of Kisangani. An increasingly ill-disciplined Ugandan army also became actively involved in massive human rights abuses in the gold-producing district of Ituri through its support for various militia groups.

But Uganda also faced a challenge at home, where, since 1986, several rebel movements have risen in the economically and socially marginalized north of the country. The most notorious of these is the Lord's Resistance Army (LRA), an exceedingly violent mystical movement led by self-proclaimed messiah Joseph Kony that initially capitalized on the Acholi tribe's loss of power in Uganda. Soon, however, the LRA's extreme brutality against Acholi populations in northern Uganda – including murder, torture, mutilations, rape, and child abductions – alienated the people Kony claimed to represent.

With poorly defined political objectives and dependent on support from the government in Khartoum for its military operations, the LRA has abducted an estimated 20,000 children in northern Uganda and forced them to serve as soldiers or sex slaves. To prevent looting and abductions, the Ugandan government created what they called protected villages, which are over-crowded, unsanitary, and dangerous internally displaced-persons camps, where millions of northern Ugandans have been forced to live. In 2002, the Ugandan government launched Operation Iron Fist in an attempt to definitively defeat the insurgency, but the operation sparked more intense and violent attacks by the LRA, dramatically increased the number of internally displaced people, and failed to end the war.

During the civil war between the Sudanese government in Khartoum and the rebel Southern People's Liberation Army, Khartoum supported the LRA, driven in part by a desire to retaliate against the Ugandan government for its support of the SPLA. Negotiations to end Sudan's 21-year civil war between the government and southern rebels led to a reduction in tensions between Uganda and Sudan in 2003, which allowed Ugandan army troops to pursue the LRA into Sudan.

In 2004, the Ugandan army enjoyed a series of successes against the LRA, and a number of senior rebel commanders took advantage of an amnesty offer to desert. But sporadic violence and abductions in northern Uganda and southern Sudan continued throughout 2005 as mediation efforts stalled.

In late 2005-early 2006, the LRA shifted their base into northeastern Congo, near Garamba National Park, reinforcing the regional dimensions of the conflict. Around the same time, the International Criminal Court unsealed arrest warrants for five LRA leaders. The ICC's actions and pressure on the battlefield led the LRA to agree to peace talks with the Ugandan government, which started in July 2006 in Juba, Sudan.