April 2002 in Guantanamo Bay, Cuba:
The US finishes building Camp Delta, a 612-unit detention center intended to replace the temporary Camp X-Ray where prisoners were held. While the transfer of prisoners went smoothly in our reality, in the alternate timeline at the start of the prisoner transfer a catastrophic failure of camp infrastructure and surveillance occurred. In the chaos, the prison break was aided by prisoners disguised as guards and allegedly orchestrated by a Cuban intelligence operative who had been in "deep cover" operating as a US Army Colonel at Guantanamo Bay for nearly a decade. Along with an unknown number of additional Cuban operatives in deep cover disguised as hispanic US service personnel who had infiltrated under the direction of the impostor Colonel, the impostors and prisoners escaped in multiple US military air, land, and sea vehicles with a significant portion of Guantanamo Bay's armaments, classified files, etc.
The caravan of escaping Cuban operatives and Guantanamo prisoners made their getaway westward to Santiago de Cuba (2nd largest city after Havana) when the US military's pursuit caught up with them. Accompanying the orders from the proper military channels was a direct video message from VP Cheney to all personnel in Guantanamo and those reinforcing them from CENTCOM, to in Cheney's words, "stop them at all costs, use overwhelming force, burn Cuba to the ground if that's what it takes. Shock and Awe."
Over the following 16 hours, the "Battle of Santiago de Cuba" between US Guantanamo forces supported by CENTCOM and the rogue Guantanamo forces supported by Cuban military had laid waste to a significant portion of the city and port, causing tens of thousands of civilian deaths, a spectacle and humanitarian disaster surpassing 9/11 a year earlier, drawing widespread condemnation from the UN and the international community. Widely considered by many to be an 'invasion' of Cuba by the US (despite its withdrawal from Santiago de Cuba back to Guantanamo Bay), the US lost significant good will around the world it had gained following the 9/11 attacks. Even the US's NATO allies declined to support the US in what they described as "a war on Cuba," distinguishing it from the war on terror in Afghanistan that they were taking part in.
A footnote to the battle itself and its aftermath, the classified files weren't destroyed in the battle, as they were soon after published in newspapers in several countries throughout Latin America amidst a wave of anti-American backlash.
The conflict was in a standoff of escalating tensions. The US and Cuban militaries were preparing for war, US and Cuban media were in full nationalism mode beating the war drums, all while Cuban and international media covered the unfolding humanitarian tragedy in Santiago de Cuba, aided by many of the G77 countries as well as Russia. An active US sea blockade of Cuba reminiscent of the Israeli blockade of Gaza also played out and was broadcast live via RT reporters embedded with the Russian food and medical aid flotilla, which when played alongside footage of the deteriorating conditions in Santiago de Cuba, added to the US's increasingly poor image in the Cuba standoff. The US government alleged the Cuban government was harboring the escaped Guantanamo prisoners, but they had not been seen since the prison break in April.
In the context of this, the Bush administration's early efforts to shift the war on terror to Iraq met swift international backlash. The domestic response to the call for war was muted once US media began showing what was happening in Santiago de Cuba, itself a spectacle of war and a deteriorating humanitarian catastrophe that we would find reminiscent of the aftermath of hurricane Katrina, although worse perhaps because the US military, instead of being the saviors, were blocking critical aid from getting to the Cuban city. When presidential advisor Karl Rove and other White House aides called a meeting with VP Cheney and President Bush urgently calling attention to Republicans' plummeting poll numbers for the upcoming November elections, the US sea and air blockade of Cuba stood down.
November 2002: US midterm congressional elections went in a landslide victory for the Democrats (on par with what we'd recognize from 2006), who argued for a return to focusing on economic issues and who were critical of the Republicans pushing the Cuba War Resolution in Congress, which failed to pass in October 2002.
In the US, the primary season for the presidential election in 2004 goes on. It's the same as we'd recognize it on the Democrats' side, although President Bush faces a primary challenge from Sen. McCain who accuses Bush of being weak on Cuba, along with McCain calling for war in Iraq (the latter mostly abandoned in mainstream US politics by this point). Facing low poll numbers, poor electoral prospects, and desperate for victories, Bush refocuses the war effort in Afghanistan, pushing for a "surge" of all available force (that we'd recognize in a lesser form from a few years later) along with increased efforts to find Bin Laden.
The US, already widely regarded as a brute on the world stage following the Battle of Santiago de Cuba, wages a brutal war in Afghanistan and the Af-Pak border region with an intensity and an enemy and civilian casualty count not seen since WW2. This effort pays off, both with the capture of Bin Laden, and the defeat of the Taliban and Al Quada in Afghanistan.
A quiet and secular Afghanistan continues economic development with a steady influx of Chinese business.
Cuba remains isolated from and highly suspicious of the US, and the economic embargo remains in place with no end in sight. Foreign aid from the G77 and Russia declined as well, leaving Cuba no better off than at the start of the century. Fidel Castro's Cold War mentality remains firm in Cuba.
The middle east and north africa remain mostly quiet as well, full of aging dictators, lacking the spark to set off an Arab Spring. Sunni-Shia relations remain as they had in the late 20th century. Isis is something from ancient Egyptian history. The Israeli-Palestinian conflict goes on.