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KABUL, Afghanistan While terrorist groups such as ISIS and the Taliban now hit headlines far more frequently than the once-dominant Al Qaeda (AQ), the Usama bin Laden-founded network remains very much alive in Afghanistan.

In fact AQ's activities in Afghanistan is part of the reason for President Trump's decision to give Defense Secretary Jim Mattis the jurisdiction to deploy more American forces to the war-torn country. An estimated 9,800 American troops are already in Afghanistan, with around 2,000 of them designated to fighting insurgent groups with AQ still a key player.

Al Qaeda is at least a few hundred strong, recently resigned Afghan Army Chief of Staff, Qadam Shah Shahim, told Fox News. They keep their operations very secret, work closely with the big groups for protection, and still pose a threat to the world.

In December, Gen. John Nicholson, Americas top military commander in Afghanistan, stated that the U.S. had killed or captured hundreds ofAQ fightersin 2016 alone and that the groups numbers were far higher than previously issued estimates. The year before, U.S. and Afghan forces together dismantledAQ networksand a large training camp in Kandahar, in what turned out to be one of the largest joint raids ever.

So 16 years since 9/11 and six years after its financier and leader Usama bin Laden was killed, how does the terror outfit still operate? Officials say AQs stamina and mild resurgence in recent years can be accredited to its ability to foster tag-team partnerships with other terrorist groups.

Al Qaeda still has a prominent role, once these networks are established, they persist, Dr. Abdullah Abdullah, the Chief Executive Officer of Afghanistan told Fox News. Just because we dont hear as much about it doesnt mean it no longer exists.

Former Afghan Army Chief of Staff, Qadam Shah Shahim (Hollie McKay/Fox News)

The attacks AQ members are involved in, he said, are these days mostly orchestrated by ISIS. The two networks are known to routinely work together, particularly in the northern provinces of Kunduz and Badakhshan, funneling fighters through the porous border from Chitral, Pakistan.

Al Qaeda and ISIS have a lot of commonalities and they share the same Salafi ideology, saidSayed Ishaq Gailani, a Sufi politician who founded the National Solidarity Movement of Afghanistan, referring to the extremely conservative arm of the Islamic religion practiced by some Sunni Muslims.

But what also keeps AQ thriving is the groups good relations with the other main jihadist players across the country; they also have cooperation agreements for access to havens in areas controlled by other terrorists.

We are seeing AQ remobilize themselves, especially in the eastern provinces of Nangarhar and Kandahar where they cooperate mostly with the Taliban, said a high-ranking official with the National Directorate of Security, the Afghan equivalent of the FBI. And now there is talk of a base in Bagram.

And in the southeastern province of Zabul, AQ is believed to operate under the umbrella of the Haqqani network (HQN), a Taliban offshoot known for its extreme brutality and rampant kidnapping for ransom. The group previously held U.S. soldier Bowe Bergdahl, and still has in custody U.S. hiker Caitlan Coleman and her husband and children.

Afghanistan CEO, Dr. Abdullah Abdullah (Hollie McKay/Fox News)

AQ provides fighters, expertise and material support to HQN when needed, intelligence officials highlighted, and several times its members have participated in joint operations with the Taliban and HQN. Furthermore, Afghan officials allege that AQs murky alliance with Pakistan remains its most fundamental lifeline as most of its training and supplies originate from the neighboring nation.

The Tehrik-i-Taliban Pakistan, often referred to as the Punjabi Taliban, is said to work directly with AQ in Pakistans federally administered tribal areas alongside the Afghanistan border. In March, U.S. forces struck and killed noted AQ leader Qari Yasin in Afghanistans Paktika province.

The Balochistan, Pakistan, native was responsible for the death of two American service members in a 2008 Islamabad hotel bombing as well as an attack on Sri Lankas cricket team the following year. Yasin was known to also have ties with the Tehrik-i-Taliban Pakistan and facilitate agreements between the two parties.

AQ additionally has merger agreements with smaller militant factions in the area, including Lashkar-e-Taiba which was founded in the mid 1980s with bin Laden funding, as well as Jaish-e-Mohammed, a Pakistan jihadist group devoted to fighting India over the state of Kashmir.

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And according to Shahim and several other intelligence officials who spoke to Fox News under the condition of anonymity, AQs leader, the 66-year-old Ayman al-Zawahri an Egyptian militant who was the longtime No. 2 and took over after bin Laden was slain by U.S. Navy SEALsis more than likely living covertly in Pakistan.

A video still of Ayman al-Zawahiri, the current leader of Al Qaeda. (AP/IntelCenter)

Sources said recent indicators of his whereabouts have focused on the remote area between the villages of Atter Shisha and Dhodial in the Khyber Pakhtunkhwa region some 23 miles north of Abbottabad, where bin Laden lived. It also was recently reported that Zawahri is possibly spending at least some of his time shielded by the population density of Pakistans largest city, Karachi.

"Zawahri continues to operate a big network, he is still very dangerous and provides the guidance and strategy, one well-placed Afghan intelligence source told Fox News. And he still enjoys Gulf state funding.

He remains at the top of the U.S. governments Rewards for Justice Most Wanted list, alongside ISIS leader Abu Bakr al-Baghdadi, with a $25 million price tag on offer for each of them to be brought to justice.

But U.S-led forces soon may have another bin Laden to contend with at the AQ helm. The slain leader's 28-year-old son Hamza has recently emerged with blessings from Zawahrias the esteemed figure to mobilize the upcoming generation of jihadists of take over the AQ helm.

Prepare diligently to inflict crippling losses on those who have disbelieved, Hamza, believed to be the 15th of bin Ladens 20 children, says softly in an audio recording that surfaced late last month. Follow in the footsteps of martyrdom seekers before you.

Picture taken from undated Al Jazeera television footage purpotedly shows Hamza bin Osama bin Laden displaying what the Taliban say is wreckage from a U.S helicopter near Ghazni. (Reuters/Al-Jazeera TV)

He goes on to explicitly signal followers to court revenge for the deaths of Syrian children killed in airstrikes by launching attacks inside America and Europe. Hamza, who is said to be married with at least two children, too is alleged to have long resided in the northwestern tribal region of Pakistan.

The DOD didn't respond to questions pertaining to Al Qaeda or its current leadership in the region, but stated that the "revised Afghanistan strategy will be presented to the President for his approval in the coming weeks."

Hollie McKay has been a FoxNews.com staff reporter since 2007. She has reported extensively from the Middle East on the rise and fall of terrorist groups such as ISIS in Iraq. Follow her on twitter at @holliesmckay

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Al Qaeda in Afghanistan: How terror group survives, thrives - Fox News