Inside Pakistan's Terror Factories: Groups and Safe Havens Under the Radar
Lashkar-e-Taiba (LeT) - The Army of the Pure
Formation and Ideology: Lashkar-e-Taiba was founded around 1987 by Hafiz Muhammad Saeed and Zafar Iqbal in Afghanistan, with support from Pakistan's ISI, as the militant wing of a Wahhabi Islamist organization Markaz-ud-Dawa-wal-Irshad. Its aim was jihad against India (particularly in Kashmir) and globally against perceived enemies of Islam. LeT's ideology is extremely fundamentalist; it justifies killing civilians as part of jihad and envisions establishing Islamic rule in South Asia.
Headquarters (Markaz-e-Taiba) - Muridke: LeT's main base is in Muridke, near Lahore, Pakistan. This huge campus, officially a "charitable" facility, includes training grounds, dormitories, and religious schools. Investigations found it was at Muridke that the 10 Mumbai attackers were trained and prepped . Post-2002 when Pakistan banned LeT formally under U.S. pressure, Lashkar renamed its social arm as Jamaat-ud-Dawa (JuD) and continued operations openly. Muridke became JuD's HQ, and Pakistan allowed it to function under the fig leaf of charity work. Inside, though, militant training often continued. When India's Operation Sindoor targeted terrorist sites, one of the key locations was Markaz Taiba at Muridke .
Training and Camps: Aside from Muridke, LeT maintained training camps in Pakistani-administered Kashmir (e.g., in Muzaffarabad and Kotli). New recruits went through a 3-week Daura-e-Sufa training (basic indoctrination), advanced weapons training (Daura-e-Aam) and specialized courses (Daura-e-Khaas). The infamous Aksa camp in Muzaffarabad was destroyed by the 2005 earthquake but later rebuilt. LeT also reportedly ran camps in the Khyber Pakhtunkhwa area for a period, under cover of "Kashmir solidarity" rallies.
State Linkages: LeT has often been called Pakistan's most loyal proxy. Unlike some others, LeT has never attacked the Pakistani state. In fact, LeT militants have acted as de facto paramilitary support for the Pakistan Army (for example, fighting alongside army units in the Kargil War of 1999 disguised as irregulars). Pakistani officials, including former President Musharraf, tacitly admitted using LeT against India. After 2001, Pakistan did detain Hafiz Saeed multiple times, but always released him after pressures eased. The ISI is widely believed to fund LeT's operations; U.S. intelligence found that ISI officers were in contact with LeT handlers during the 26/11 Mumbai attack, guiding them . Though Pakistan denied official involvement).
Key Figures:
Hafiz Muhammad Saeed - Co-founder and emir of LeT/JuD. UN-designated terrorist. Despite his international notoriety, lived openly in Lahore for years, delivering sermons and rallying fighters. He was placed under house arrest off and on. In 2020, under FATF pressure, Pakistan convicted Saeed on terror financing charges, sentencing him to prison. However, many suspect this is more show than substance; whether he remains actually incarcerated is unclear.
Zaki-ur-Rehman Lakhvi - LeT's operations chief, mastermind of the Mumbai 2008 attacks. Arrested in 2009 in Pakistan, but his trial stalled and he was released on bail in 2015, allegedly continuing LeT operations on the side. In January 2021, again under global pressure, Pakistan sentenced Lakhvi to a nominal jail term for terror financing. Still, his whereabouts are murky; India suspects he remains involved with LeT's militant planning.
Abdul Rahman Makki - Brother-in-law of Hafiz Saeed, senior JuD leader. Designated terrorist by US and UN. Pakistan kept him under preventive detention intermittently. Makki's fiery speeches raised funds for jihad; he is considered the propaganda chief.
LeT's offshoot Falah-e-Insaniyat Foundation (FIF) was ostensibly a relief organization, especially active during disasters (like a 2005 earthquake, 2010 floods). But the U.S. Treasury exposed FIF as a front financing LeT's terror . Pakistan banned FIF in 2019 finally.
Jaish-e-Mohammed (JeM) - The Army of Mohammed
Formation and Ideology: Jaish-e-Mohammed was formed in early 2000 by Masood Azhar, a radical cleric released from Indian prison in exchange for hostages of the IC-814 flight hijacking in 1999. Based in Bahawalpur, Pakistan, JeM espouses an extremist Deobandi ideology, similar to the Taliban, and focuses on violent jihad to "free" Kashmir and attack India, as well as anti-Western and anti-Israel rhetoric.
Headquarters - Bahawalpur: JeM's base of operations is in the city of Bahawalpur in Punjab province. Azhar's family madrasa, Madressah Usman-o-Ali, became a JeM recruiting center. JeM built at least two major complexes there: one often cited is the Markaz Subhan Allah in Bahawalpur, which Indian intelligence identified as a key center . Indeed, one of the terrorists killed in Operation Sindoor, Hafiz Muhammed Jameel, was noted to supervise operations at Markaz Subhan Allah . Another JeM facility near Bahawalpur was targeted by an airstrike in 2019 (though India hasn't confirmed hitting Bahawalpur, only Balakot).
Bahawalpur is effectively off-limits to outside investigators. Even Pakistani journalists tread carefully around JeM's stronghold. The fact that Azhar reportedly lives there under ISI protection indicates how secure JeM is within Pakistan.
Training Camps: JeM established camps in Pakistan's part of Kashmir as well as in Pakistan's Khyber Pakhtunkhwa. One known camp was in Balakot (the one struck by IAF in 2019), set up in a mountainous forested area to train cadres in combat and fidayeen attacks. Pre-2001, JeM also operated camps in Afghanistan's Taliban-controlled territories. After 9/11 and Pakistan's ostensible U-turn, JeM relocated more to mainland Pakistan. Azhar's group also ran several mosques and madrasas across Punjab and Sindh for recruitment and fundraising.
Key Figures:
Maulana Masood Azhar - Founder and leader of JeM. Despite being one of the world's most wanted terrorists (UN listed, India's most wanted), Azhar has rarely been seen in public in recent years. Following the 2001 Parliament attack, Pakistan detained him briefly then released him. He is believed to be frequently "kept in hiding" by ISI, especially when global pressure mounts. For instance, during FATF scrutiny, Pakistan claimed Azhar couldn't be found; then reports emerged he was in Pakistani military hospital during illness. His voice recordings and writings still surface, inciting jihad.
Abdul Rauf Asghar - Masood Azhar's brother, a senior JeM commander who reportedly handles day-to-day operations. Rauf was implicated in the IC-814 hijacking and later masterminded several attacks. In the current context (2025), rumors suggest he might have been hit in Operation Sindoor or subsequent Indian actions , although confirmation is lacking.
Ghazi Baba - (Real name: Shahbaz Khan) JeM operational commander in early 2000s, architect of Parliament attack, killed by Indian forces in 2003 in Kashmir. Many like him, who were Pakistani nationals leading terror ops in Kashmir, illustrate JeM's direct role in attacks.
Omar Saeed Sheikh - Though not a JeM cadre, this British-Pakistani militant (freed alongside Azhar in 1999) became affiliated with JeM and later involved in the murder of journalist Daniel Pearl (2002). Some accounts suggest JeM members had overlapping membership with Al-Qaeda (Omar Sheikh allegedly even wired money to Mohamed Atta before 9/11).
State Linkages: JeM has a more contentious relationship with the Pakistani establishment at times than LeT does, mainly because JeM members twice attempted to assassinate General Musharraf in 2003 after he cracked down under U.S. pressure. However, Pakistan never truly dismantled JeM - it reined them in when needed but kept them as an India-focused tool. JeM's periodic banning has been ritualistic. Azhar was mysteriously "detained" after the 2019 Pulwama attack and Balakot strike, only to apparently be let be afterwards. China blocked Azhar's UN terrorist listing for years on Pakistan's request, highlighting Pakistan's shielding via allies.
JeM's fighters often collaborated with the Afghan Taliban and Al-Qaeda. There were reports that some JeM cadres fought alongside the Taliban against U.S. forces. Yet Pakistan allowed JeM to recruit and run madrassas, calculating that keeping them aimed at India was the lesser evil.
JeM is also known for pioneering fidayeen suicide attacks in Kashmir - the first suicide bombing in Kashmir (April 2000) was by a Briton recruited by JeM. They repeated this tactic, culminating in the Pulwama 2019 suicide attack. Such capabilities point to high motivation and training imparted by the group - and raises questions how such explosives were acquired (usually RDX sourced from Pakistani or Afghan military stock).
Other Groups and Safe Zones
While LeT and JeM are the principal anti-India proxies, there are other groups and areas:
Hizbul Mujahideen (HM): Although primarily composed of Kashmiris, HM operates from Pakistan (Muzaffarabad). Its chief Syed Salahuddin is based there. Pakistan formally banned HM in 2019 after US designated Salahuddin, but in practice HM offices function and Salahuddin roams free . HM has historically had training camps in PoK with tacit Pak support.
Al Badr, Harkat-ul-Jihad al-Islami (HuJI), Harkat-ul-Mujahideen (HuM): These smaller jihadist outfits also had bases in Pakistan. HuM's leader Fazlur Rehman Khalil even signed Osama bin Laden's 1998 fatwa against the West. Pakistan has at times co-opted or curtailed these groups as needed.
Karachi: The megacity Karachi has been a hideout for many terrorists due to its size and anonymity. From Dawood Ibrahim (an Indian mafia don wanted for 1993 Mumbai blasts, believed to be sheltered by ISI in Karachi's upscale Clifton area) to sleeper cells of LeT, Karachi is a safe haven. Pakistani authorities typically deny Dawood's presence, but global agencies list his Pakistani passports and residences.
Quetta and Peshawar: More for Afghan-focused groups (Taliban, Haqqanis), but these cities also hosted crossover militants. E.g., certain Kashmiri insurgents took refuge in Quetta alongside Taliban after facing heat post 2001.
The picture that emerges is a country dotted with enclaves of terrorist activity:
Formal bans versus Ground Reality: Pakistan's interior ministry might proscribe a group under pressure, but the group's leadership and cadre often rebrand or lay low until pressure lifts. For instance, LeT -> JuD -> FIF; JeM sometimes used the name Khuddam ul-Islam; HuM once became Ansar ul-Ummah, etc.
Areas off-limits to foreign scrutiny: Journalists and international observers are often restricted from areas like Muridke, Bahawalpur, or parts of PoK - the very places where these terror infrastructures sit. Meanwhile, Pakistani propaganda tries to maintain plausible deniability.
In essence, Pakistan's "terror factories" - from Lashkar's Muridke headquarters to Jaish's Bahawalpur compounds - have operated with varying degrees of cover but largely with the indulgence of the state. Until these factories are irrevocably shut down and their owners held accountable, the threat of terrorism emanating from Pakistan remains alive. Operation Sindoor, which took out some of these very assets , underscores that India is no longer content with mere dossiers - it is willing to strike those factories at source if Pakistan doesn't act.