This Asia Times article digs down into the roots of the jihadi story. Fascinating, but it reads as though it was published by an intelligence service, presumably Indian. Be good to read a cross-checked version of this.
It does sound as though we're entering a new stage in this conflict.
KARACHI - The recent arrest of two top Pakistani jihadis, Maulana Fazalur Rehman Khalil and Qari Saifullah Akhtar, marks the beginning of the end of an era that started in the mid-1980s when the dream of an International Muslim Brigade was first conceived by a group of top Pakistan leaders.
The dream subsequently materialized in the shape of the International Islamic Front, an umbrella organization for militant groups formed by Osama bin Laden in 1998 and loosely coordinated by the Lashkar-e-Toiba (LET) of Pakistan.
The arrests in Pakistan, made under relentless pressure from the United States, are aimed at tracing all jihadi links to their roots, which are mostly grounded in Pakistan's strategic core.
As a former Pakistan Inter-Services Intelligence (ISI) operator and air force official, Khalid Khawaja, commented in the Pakistani press on the arrests of the two jihadis, "Every link of the arrested jihadi leaders goes straight to top army officials of different times."
... The present problems in the "war on terror" are linked to the labyrinth of groups developed during the decade-long Afghan resistance to the Soviet occupation of Afghanistan in the 1980s. The US Central Intelligence Agency (CIA) sponsored much of the jihadi movement, using the ISI as a front and a conduit.
For example, US planes used to fly supplies, arms and ammunition for the Afghan fighters to Islamabad, from where they were transferred to the ISI Afghan cell's facility at Rawalpindi, from where the ISI had its own network to distribute the merchandise to the mujahideen groups of its choice.
This modus operandi exposed a serious flaw in US strategic thinking. By not dealing directly with the Afghan groups, the US had no control over which ones benefited, and invariably only those factions that were both anti-Western capitalism and anti-Soviet socialism were cultivated by the ISI.
In this environment, late Pakistani dictator General Zia ul-Haq and his closest associate, the then director general of the ISI, Lieutenant-General Akhtar Abdur Rehman, both of whom died in a plane crash in 1988, saw their opportunity to lay the foundations for a global Muslim liberation movement.
Blissfully unaware of this perspective, the CIA supported Pakistani efforts to recruit Muslim youths from the Pacific to Africa, and a whole generation of youngsters was trained in jihadi, and, importantly, with strong anti-US overtones. Youngsters were drawn from groups such as Abu Sayyaf from the Philippines and Muslims from Arakan province in Myanmar.
To keep the movements under the strict control of the ISI, the ISI established proxies such as al-Badr, the Harkat-i-Jihad-i-Islami and Harkatul Ansar (or Harkatul Mujahideen as it was once known). Akhtar, incidentally, was leader of Harkat, while Khalil was head of the Harkatul Ansar.
Crucially, all this was done without the CIA and, for that matter, the leaders of the Islamic movements knowing just how much control the ISI actually had.
To keep the Arab movements under control, an al-Badr facility was organized in Khost province in Afghanistan. A dynamic law and master of arts graduate from Karachi University, Bakhat Zameen Khan, a member of the Jamaat-i-Islami (JI), a powerful religious party (who originally hailed from Dir in North West Frontier Province), was chosen as commander. He brought together all Arab jihadis at the facility, and linked senior ones to the ISI. Out of this camp, the Palestinian Hamas emerged, as well as the Arab-sponsored Moro liberation movement led by Abu Sayyaf...
... Former Afghan prime minister and legendary mujahideen Hekmatyar went into exile in Tehran once the Taliban came to power in 1996. But as the Taliban regime disintegrated in late 2001, the US put pressure on Tehran to expel Hekmatyar, planning to arrest him as soon as he returned to Afghanistan, where he believed he could reinvent himself as an anti-US resistance guerrilla leader.
By this time, though, Islamabad, having been persuaded to abandon the Taliban and join the United States' "war on terror", was in the process of finding a substitute connection in Afghanistan. Hekmatyar was the obvious choice. Khan was sent to Tehran to assure Hekmatyar of Pakistan's support should he return to Afghanistan.
Al-Badr members were tasked to escort Hekmatyar from Iran to Afghanistan and to keep him away from the Americans. He was kept in a safe house in Chitral, where al-Badr members, along with Pakistan commandos, guarded the premises. As soon as al-Badr members located other diehard HIA commanders, such as Kashmir Khan and Ustad Fareed, Hekmatyar was launched in Afghanistan's Kunar province to reorganize the HIA as a proxy of the ISI in Afghanistan.
Meanwhile, al-Badr, with its long experience in the region, helped many Arabs and their families, desperately wanted by the US, by providing them shelter and arranging fake passports for them to return to their countries of origin.
From the mid-1980s, then, to the present the ISI and al-Badr have virtually been one and the same thing. The US State Department declared al-Badr a terrorist organization a few years ago, and has steadily put pressure on Islamabad to arrest its operators. However, Pakistan, for obvious reasons, has been reluctant to comply with US demands....
... However, after the then director general of the ISI, Lieutenant-General Mehmood Ahmed, retired the day the US attacked Afghanistan, Khalil returned to Pakistan and was placed under house arrest as Islamabad had done an about-turn, under US insistence, on support for the Taliban.
The ISI, jihadi leaders and the Pakistani army have over the years been inextricably linked, especially in Afghanistan. Now that two key jihadi figures, Khalil and Akhtar, have been arrested, it can easily be deduced that the story of their involvement, and the quest to stamp out the jihadi movement at its heart, will not end with them being incarcerated: there has always been someone in the Pakistani establishment, whether active or retired, to pull the strings, as was the case with Khalil and Akhtar, and with Bakhat Zameen Khan.
Now, with the arrest of the the jihadi leaders, the "cover" has been broken and there is little place left for the "operators behind the scenes" to hide.
"The cat is cornered against the wall and the much-awaited game within the army is about to start," commented an observer based in Washington.
Emphases mine. Talk about building a monster.
The Pentagon is looking at funding "friendly militias" to operate in the world's ungoverned regions. I hope they've learned something from the CIA's "successes".
This backstory makes that plane crash even more interesting.