Inside Kenya’s silent war: The secret battle against terror in Boni Forest and beyond

It is a conflict that has claimed lives, displaced communities, and tested Kenya’s national resolve. But quietly, and often without public attention, Kenya has been fighting back.

It began with blood. In January 2019, the nation was jolted awake when terrorists struck the DusitD2 complex in Nairobi, killing 21 people and injuring dozens. From Mandera to Garissa, Wajir to Lamu, Kenya witnessed a deadly surge in attacks.

Civilians, police officers, and foreign aid workers became regular targets. But the ripple effects stretched further—crippling cross-border trade, straining diplomacy, and igniting fears of instability throughout the Horn of Africa.

In response, the National Intelligence Service (NIS) shifted gears. Operating in secrecy, they unleashed one of their most guarded weapons: the Special Operations Group (SOG)—an elite multi-agency unit trained to operate in the toughest conditions, far from public view.

Only 5% of applicants make it through the SOG program. The training is grueling—designed to reshape civilians into covert warriors capable of dismantling terror cells, intercepting improvised explosive devices (IEDs), and defending Kenya’s porous borders.

In October 2024, it was SOG officers who discovered a stockpile of weaponized gas cylinders in Ijara, neutralizing a major threat before it reached its target.

For the first time in decades, Kenya’s spy agency has granted the media unprecedented access—lifting the veil on a force long shrouded in mystery. Our journey took us to the National Intelligence

Training Center, a highly restricted facility where recruits undergo rigorous training—ranging from classroom-based surveillance theory to paramilitary drills in unforgiving terrain.

And then, we flew to the frontlines.

Above the thick canopies of Boni Forest, a military helicopter hovers at treetop level—its rotor blades slicing through the coastal air. On board, elite officers scan the ground for threats. Beneath us, operating bases sit nestled in enemy-prone territory—silent fortresses where some of Kenya’s most dangerous missions begin.

Fifty-five kilometers northeast, near the volatile Kenya–Somalia border, lies a Forward Operating Base (FOB)—a hub for offensive operations and a deterrent against Al-Shabaab incursions. Just 100 meters south, another outpost guards vital land and maritime routes. Together, they form a ring of steel along one of East Africa’s most dangerous corridors.

The war, however, is not fought by bullets alone.

It is in places like Masalani—a new operational frontier—that Kenya’s multi-agency force confronts both terror networks and geography. “This isn't just defense—it’s disruption,” says Faris Etundo, Commander of Tactical Operations. “Our aim is to shatter their supply and recruitment chains before they reach Kenya.”

Masalani protects more than security—it guards the LAPSSET corridor, a lifeline for regional trade. Here, HUMINT—Human Intelligence—is the cornerstone. Embedded agents operate within local communities, turning whispers into actionable intel. Local residents, once skeptical, are now allies in the mission. Despite murmurs from a few political figures, many locals have embraced this shift, recognizing its potential to open up the north and bring long-absent development.

To the north, the once-hostile outpost of Holugo, 17 km from the Somalia border, is being rehabilitated. Roads have returned. Trust is being rebuilt. In Raaskamboni, deep inside Somali territory, a base once under Al-Shabaab control is now jointly held by Kenyan and Jubaland forces. Women cross the border for firewood—fear has given way to freedom.

In an exclusive interview, a 23-year-old SOG officer, the youngest in his squad, tells us what success looks like: three years of zero infiltration. That, he says, is Kenya’s new doctrine—take the fight to the enemy before the enemy brings it home.

At the heart of this war is the Intelligence Operations Centre, where real-time data guides missions. Since the operation began, over 377 firearms have been seized—including M6s, AK-47s, FN rifles, and bomb-making components. Each seizure, each intercepted plot, is a battle won.

Meanwhile, in Kenya’s twin capitals—Nairobi and Mombasa—which once bore the brunt of terror attacks, calm has returned. Not a single major incident has been reported in over two and a half years—a testament to the silent sentinels working in the shadows.