The penultimate scene in the recently released film Captain Phillips, about the 2009 seizure of the US-flagged cargo ship Maersk Alabama by Somali pirates, depicts the methodical precision with which a Navy SEAL Team 6 unit identified and then captured or killed the pirates during their doomed attempt to ferry their hostage to the Somali mainland.

According to Jeremy Scahill’s new book Dirty Wars, the crisis over the Maersk Alabama was the newly inaugurated President Barack Obama’s introduction to the formidable surveillance and intervention capabilities of the US military’s clandestine Joint Special Operations Command (JSOC), which commands the military’s most elite commando units such as the Navy’s SEAL Team 6 and the Army’s Delta Force. After the September 11, 2001 attacks, Defense Secretary Donald Rumsfeld and Vice President Dick Cheney oversaw the expansion of JSOC into a shadowy manhunting army that could “find, fix and finish” alleged terrorist enemies around the world without Congressional oversight or public discussion. But following the Maersk Alabama operation, according to Scahill, President Obama “let JSOC off the leash” by expanding authorization for JSOC’s clandestine operations into previously off-limits areas and countries beyond the official battle zones of Iraq and Afghanistan.

Obama’s embrace of JSOC’s manhunting capabilities was on display in early October of this year with a pair of highly publicized raids in Libya and Somalia intended to capture alleged terrorist masterminds in Africa. The strikes were carried out by elite JSOC special mission units and were approved and overseen by President Obama, who was given regular updates. In one attack, JSOC commandos from the Army’s Delta Force snatched Abu Anas al-Libi -- an alleged al-Qaeda leader wanted for his involvement in the 1998 embassy bombings -- off the streets of Tripoli, Libya. Earlier that day, SEAL Team 6 operators assaulted a beachside villa in Barawe, Somalia, hoping to arrest the al-Shabaab operative “Ikrimah,” linked to the deadly attack on a Kenyan shopping mall. The SEALs were forced to turn back following a protracted gunfight.

Despite President Obama’s assurances in an important May 2013 speech that he rejected the concept of “perpetual war” and would seek to eventually bring the war against al-Qaeda to an end, the concurrent JSOC raids across the African continent illustrate a deepening institutionalization and expansion of the ongoing global shadow war the United States is waging against alleged Islamist terrorists and their “associates.”

Most immediately, the centrality of the US Special Operations Forces in these operations rather than the CIA using drones illustrates the continuing shift in the center of gravity for shadowy counterterrorism operations away from the CIA to the US military and its clandestine operators. The Obama administration has been stung by fierce criticism of CIA drone strikes, which critics condemned as an unlawful global assassination program. These two Africa operations thus appear intended to illustrate a broader Obama administration initiative to shift counterterrorism operations toward US military commands, which in theory provide “additional layers of accountability and oversight,” and put them under “a more disciplined command culture,” as James Kitfield writes. The shift to military control and away from drone strikes also implies a greater emphasis on capture instead of killing, though this may not necessarily be the case. Moreover, as Kitfield notes, during his March confirmation hearings to become CIA director, the leading architect of the CIA drone program, John O. Brennan, expressed his desire to move the drone program and paramilitary operations from the CIA back to the US military in order to return the agency’s focus to its traditional role of intelligence gathering and analysis. Nevertheless, an analysis by Foreign Policy suggests that the effort to remove the CIA from targeted killing and drone strikes is running into some obstacles due to the need for “agility” and deniability in the face of intense local opposition to such strikes in Pakistan, among other places.

More broadly, the two JSOC strikes shed light on the sweeping extension and institutionalization of the US military’s manhunting capabilities and operations across the African continent, in addition to its manhunting networks in Central and West Asia. Nick Turse has outlined the expansion of base construction, advisory deployments and Special Operations missions across the continent under the aegis of the US military’s Africa Command (AFRICOM), established in 2007. AFRICOM’s primary mission is counterterrorism and the Special Operations Command Africa has been a major player in establishing a network of bases and logistical sites to support various “high-risk activities” carried out by elite forces from Joint Special Operations Task Force-Trans Sahara operating in North Africa as well as the quick response force known as Naval Special Warfare Unit 10 that operates closer to the Horn of Africa. In this context, it appears that JSOC forces have undertaken their own “Berlin Conference” division of the African continent into separate manhunting sectors that mirrors the JSOC’s earlier division of Southwest Asia. Following September 11, the Navy’s SEAL Team 6 became the most active JSOC element in Afghanistan and Pakistan while the Army’s Delta Force became the JSOC force most responsible for Iraq. Similarly, as seen in these two operations, it appears that the US Army’s Delta Force has responsibilities for North Africa, while the Horn of Africa is Navy SEAL territory.

And lastly, the JSOC raids in Africa illustrate the further blurring of international and domestic counterterrorism agencies and authorities within the global manhunting infrastructure. One of the central organizational developments making possible global manhunting operations has been the emerging Joint Task Force model of interagency coordination and information sharing among the US military, the CIA, the FBI and other organizations into a seamless network across domestic and international authorities. It appears that both CIA and FBI agents played a role in the Libya and Somalia operations, linking with the US military in its kill/capture operations and in developing intelligence for targeted strikes. This blurring of boundaries between domestic and international counterterrorism and manhunting takes on a disturbing quality in light of NSA whistleblower Edward Snowden’s revelations that the NSA has played a major role in assisting the targeted killing programs undertaken by both the CIA and the American military, in which data swept up from global communications networks, including those of American citizens, has been used to generate target packages for lethal operations in the global shadow war. The NSA has set up a special unit, the CounterTerrorism Mission Aligned Cell or CT Mac, to use its phone and e-mail interceptions to pinpoint the coordinates for CIA and US military drone strikes. It is possible, though it has not been proven, that NSA interceptions could also be used by the Department of Homeland Security or the FBI in targeting domestic threats or opponents.

Thus, although Obama’s May speech articulated an important recognition of the dangers of “perpetual war,” the Obama administration continues to streamline and institutionalize the highly classified practice of targeted killing and the rendition practices of the Bush administration, transforming ad hoc elements into an integrated and synergistic counterterrorism infrastructure capable of sustaining a permanent war across several continents as well as across domestic and international authorities. But rather than the CIA and its drones serving as the tip of the spear in this permanent war, it will increasingly be the clandestine “ninjas” of JSOC and their individually targeted and networked kill/capture model of counterterrorism that is in the lead. As Peter Bergen recently pointed out, a sign of where the Obama administration is placing its bets about the future of warfare is that while there are major cuts planned for all four of the armed services, Special Operations Command is one of the few places in the military where the force is actually growing. Although no longer named as such, the “global war on terrorism” is a long way from ending.

This post has been modified slightly from its original version.