The Secret War That Shaped 40 Years of Conflict

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INTRODUCTION: THE SPY AGENCY THAT SHAPED A NATION NEXT DOOR

Most people know Afghanistan for two things: long wars and foreign armies. But behind almost every big moment—Soviet invasion, civil war, the rise of the Taliban, and even America’s withdrawal—there has been one quiet but powerful actor in the shadows:

Pakistan’s ISI (Inter-Services Intelligence).

The ISI didn’t just influence Afghanistan.
For 40 years, it helped build military groups, shape governments, and sometimes even break them.

This is the story of how a spy agency next door became one of the most powerful forces in Afghanistan’s history—sometimes as a protector, sometimes as a manipulator, and often as the invisible hand pushing events forward.

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SECTION 1: THE BIRTH OF A SECRET WAR (1979–1989)

1.1 The Soviet Invasion and the ISI’s Golden Moment

When the Soviet Union invaded Afghanistan in 1979, Pakistan suddenly became the frontline state of the Cold War. The U.S. and Saudi Arabia needed someone on the ground to organize Afghan rebels—the Mujahideen.

They chose the ISI.

For Pakistan, this was a dream come true:

• Billions in American and Saudi money
• Full control of training camps
• Ability to choose which Afghan groups would rise to power
• A chance to shape Afghanistan’s future

The ISI created a system:

• Weapons in from the U.S.
• Money in from Saudi Arabia
• Fighters out to Afghanistan

But the ISI made one big choice that shaped the future:

They favored the most hardline Islamist factions.

Why?

Because they believed Afghanistan must never fall under India’s influence.
A friendly, Islamist government would be loyal to Pakistan.

This decision would echo for decades.

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1.2 The Rise of Gulbuddin Hekmatyar

The ISI’s favorite warlord was Gulbuddin Hekmatyar, a fierce Islamist leader known for brutality.

He received:

• The largest share of U.S. weapons
• ISI protection
• Training camps
• Money channels

But Hekmatyar never won the hearts of Afghans.

ISI had chosen strength over popularity—an early warning of future mistakes.

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1.3 Victory Over the Soviets, Chaos After

By 1989, the Soviets withdrew. ISI celebrated.
But a new problem emerged:

Who would control Afghanistan now?

ISI tried to install Hekmatyar.
Other Mujahideen leaders resisted.
Civil war broke out.

ISI had helped the Afghans win against a superpower
—but had not built a stable future.

This would not be the last time.

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SECTION 2: THE TALIBAN RISE FROM THE ASHES (1994–2001)

2.1 Afghanistan Collapses Into Civil War

After the Soviets left, Kabul became a battlefield.
Warlords shelled cities, robbed civilians, and fought for power.

Pakistan’s ISI feared two things:

1. Afghanistan breaking into pieces
2. India gaining influence through other factions

They needed a new force—disciplined, loyal, and strong.

They found them in the refugee schools of Pakistan.

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2.2 The Taliban Appear

The Taliban started as young religious students in Pakistan’s border areas.
Most had grown up in refugee camps.
Many studied in Pakistani religious schools funded by Saudi money.

The ISI saw an opportunity.

They provided:

• Training
• Weapons
• Safe routes
• Trucks and fuel
• Advisors

With ISI support, the Taliban swept across Afghanistan.

By 1996, they took Kabul.

Pakistan became the first country to recognize the Taliban government.

ISI had finally created the “friendly regime” it always wanted.

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2.3 The Taliban’s Strict Rule

Under Taliban rule:

• Girls’ schools were shut
• Harsh punishments were enforced
• Rival ethnic groups were crushed
• Al-Qaeda found a new home

For Pakistan, things seemed stable.
For Afghans, daily life became much harder.

But the biggest problem was still hidden:

ISI never fully controlled the Taliban.
And inside Afghanistan, resentment grew.

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SECTION 3: 9/11 CHANGES EVERYTHING (2001–2014)

3.1 The U.S. Arrives and Flips the Chessboard

After the 9/11 attacks, America invaded Afghanistan.
The Taliban fell within weeks.

Suddenly, ISI’s 20-year project was destroyed.

Pakistan told the U.S.:

“We will help you fight terrorism.”

But behind the scenes, things were more complicated.

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3.2 ISI’s Two-Track Strategy

Pakistan supported the U.S.—officially.
But it also kept contact with:

• Taliban leaders
• Haqqani Network
• Other insurgent groups

Why?

Because Pakistan feared:

• A strong Afghan government tilting toward India
• A long-term U.S. presence on both of Pakistan’s borders
• Losing influence in Kabul

3.3 The Safe Havens Problem

Taliban and Haqqani leaders fled into Pakistan’s tribal areas.

They found:

• Safe houses
• Medical care
• Training camps
• Ability to regroup

From these sanctuaries, they rebuilt their forces.

U.S. commanders often said:

“We cannot win a war where the enemy can rest on the other side of the border.”

And they were right.

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SECTION 4: THE HAQQANI NETWORK—ISI’S MOST POWERFUL ALLY

Among all groups ISI supported, one was the most effective:

The Haqqani Network

Led by the Haqqani family, they ran:

• Cross-border raids
• Suicide attacks
• Kidnapping networks
• Business operations
• Taliban diplomacy

The ISI saw them as reliable partners.

The U.S. saw them as the deadliest force in the war.

The Haqqanis eventually became:

• Taliban’s military backbone
• Controllers of Kabul’s security
• Kingmakers in Afghan politics after 2021

This was ISI’s long game—and it worked.

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SECTION 5: THE U.S. WITHDRAWAL AND ISI’S FINAL CHECKMATE (2018–2021)

5.1 The Doha Agreement Weakens Kabul

When the U.S. began peace talks with the Taliban in Doha, Pakistan helped bring the Taliban to the table.

But Kabul’s government was excluded.

This decision:

• Boosted Taliban morale
• Crushed Afghan military confidence
• Showed the world the Taliban were legitimate
• Placed Pakistan back at the center of Afghan politics

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5.2 The Fall of Kabul

When the Taliban launched their final offensive in 2021, Afghan forces collapsed in 11 days.

ISI-trained networks played key roles:

• Taliban units swept through the south
• Haqqanis took Kabul
• Pakistan’s intelligence chief (Lt. Gen. Faiz Hameed) arrived in Kabul days later to help form the new government

Pakistan had finally regained a friendly Afghanistan.

But new problems emerged.

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SECTION 6: HOW ISI’S STRATEGY BROKE AFGHANISTAN TOO

Even though ISI secured long-term influence, Afghanistan paid a huge price.

6.1 Four Decades of War

By supporting armed groups, ISI helped keep Afghanistan in a constant state of conflict.

6.2 Weak Governments

No Afghan leader could stand strong while Pakistan favored militant alternatives.

6.3 Ethnic Tensions

ISI-backed groups were mostly Pashtun, increasing divisions with Tajiks, Hazaras, and Uzbeks.

6.4 Taliban 2.0 and International Isolation

Pakistan helped the Taliban return—but the new regime is isolated and unrecognized, creating:

• Economic collapse
• Humanitarian crisis
• Security risks

6.5 The Monster Pakistan Can’t Control

The irony?

Some groups ISI once supported now attack Pakistan itself.

Especially the Pakistani Taliban (TTP), who share roots with the Afghan Taliban.

Pakistan built a network so powerful…
that parts of it slipped out of control.

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SECTION 7: WINNERS AND LOSERS OF ISI’S LONG GAME

Winners

• Pakistan’s military (short-term influence)
• Taliban (control of Afghanistan)
• Haqqani Network (key positions in Kabul)

Losers

• Afghan civilians (40 years of war)
• Afghan women (rights rolled back)
• Afghan economy (global isolation)
• Regional stability
• Pakistan’s own internal security

ISI won influence—but at massive cost.

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SECTION 8: CONCLUSION — A SUPERPOWER IN THE SHADOWS

For 40 years, Pakistan’s ISI shaped Afghanistan more than any other force besides the U.S. and USSR.

It:

• Built the Mujahideen
• Raised the Taliban
• Played both sides during the U.S. war
• Helped engineer the Taliban’s return
• Became the most influential foreign actor in Afghanistan

But its strategy also helped prolong violence, weaken institutions, and create long-term instability that affects both nations today.

Citations

Afghanistan’s story is not only about the big powers.
It is also about the hidden hands in the shadows—
and no hand was more active than Pakistan’s ISI.

Council on Foreign Relations, “The ISI and Terrorism: Behind the Accusations” — explains ISI’s links to Afghan militant groups, including the Taliban and Haqqani Network. Council on Foreign Relations

India Today, “ISI has links with militants: Musharraf” — outlines former Pakistani President Musharraf’s admission about ISI using Haqqani influence. India Today

India Today, “ISI paid Haqqani Network $200,000 to fund bombing” — based on U.S. diplomatic cables. India Today

FDD Long War Journal, “Admiral Mullen: Pakistani ISI Sponsoring Haqqani Attacks” — U.S. military leadership accusing ISI of supporting Haqqani operations. FDD

Counter Extremism Project, “Afghanistan: Extremism & Counter-Extremism” — detailed report on Haqqani Network’s role among militant groups and ISI ties. Counter Extremism Project

India Today, “How Pakistan’s ISI is fuelling Haqqani-Taliban infighting” — on ISI strategy to maintain influence through Haqqani within Taliban. India Today

Inter-Services Intelligence activities in Afghanistan, Wikipedia — summary of ISI’s covert role in Afghanistan across multiple decades. Wikipedia