“You who have ruled India for eight hundred years, you who lit the flame of the one true God in the darkness of polytheism: how can you remain in your slumber when the Muslims of the world are awakening?” the al-Qaeda ideologue Asim Umar asked India’s Muslims last summer. “If the youth of the Muslim world have joined the battlefields with the slogan ‘Shari’a or Martyrdom,’ and put their lives at stake to establish the Caliphate, how can you lag behind them? Why is there no storm in your ocean,” Mr. Umar demanded to know.

Last week’s arrests of key Indian Mujahideen operatives have led to speculation that India’s most feared terror group — responsible for savage serial bombings in major cities, including the 2006 attacks on Mumbai’s suburban train system — may be disintegrating. Tehseen Akhtar, its key recruiter, is now in prison; so is Muhammad Zarar Siddibapa, its operation chief.

For investigators though, these breakthroughs have brought forth disturbing new evidence that Mr. Umar, and other propagandists like him, are succeeding in calling a new army into being — an army born in Indian towns and cities scarred by communal warfare and hardened in the battlefields of Pakistan’s north-west.

The dusk that shrouds the Indian Mujahideen heralds, the evidence suggests, the coming of its second sunrise.

The new jihadisKarachi residents Muhammad Fahim and Muhammad Abdul Walid, held by the Uttar Pradesh police last week, told investigators that they had first been recruited by the Lashkar-e-Taiba, and then broke with it to make their way to a Taliban training camp in Afghanistan’s southern Helmand district. Then, they were led by the fugitive Pune jihadist, Mohin Chaudhury to the Indian Mujahideen’s Karachi-based chief, Riyaz Shahbandri. Faisalabad-based bombmaker Zia-ur-Rahman, Mr. Akhtar’s recently arrested deputy, served with Taliban groups in Pakistan’s Punjab before volunteering to serve with the Indian Mujahideen fighting across the border.

Meanwhile, new jihadist cells have sprung up within India. The recruits include young people, their minds fired by Internet Islamism, as well as veterans once linked to the proscribed Students Islamic Movement of India (SIMI). Fugitive Ranchi resident Haider Ali, the National Investigation Agency (NIA) says, raised volunteers from both these groups for the bombing of the revered Buddhist shrine at Bodh Gaya last year, as an act of vengeance for communal violence against Myanmar’s Rohingya Muslim minority.

Mr. Ali’s cell, only loosely connected through him to the Indian Mujahideen, followed up that attack with an attempt to assassinate Gujarat Chief Minister Narendra Modi at a rally in Patna, surprising the organisation’s leadership in Karachi.

In Tamil Nadu, volunteers at a Chennai college even signed up to serve with jihadists in Syria — recruited by local Islamists, and financed by a Singapore-based executive.

Key commanders of the Indian Mujahideen, meanwhile, remain active in Karachi, most important of them being Riyaz Shahbandri, his brother Iqbal Shahbandri and Abdul Subhan Qureshi. There are a host of second-rung leaders still at large, like Mirza Shadab Beg, Shahnawaz Alam, Muhammad “Bada” Sajid, Alamzeb Afridi, Zulfikar Fayyaz “Kagazi,” Rahil Sheikh and Ariz Khan. The man who financed them all, ganglord Amir Raza Khan, is also at large.

The western stormFrom Internet chats between Mr. Shahbandri and Mr. Siddibapa, recovered by the NIA, we know that several of those men have sought combat training with jihadists in Pakistan’s north-west, and in Afghanistan, developing skills the Indian Mujahideen’s cadre never had.

It has long been evident that the gathering storm of violent Islamism in Pakistan would lash India, too. In 2010, al-Qaeda released a posthumous audio message from Egyptian jihadi Said al-Masri, claiming responsibility for the bombing of the German Bakery in Pune. “The person who carried out this operation was a heroic soldier from the Soldiers of the Sacrifice Brigade, which is one of the brigades of Qaedat al-Jihad [the al-Qaeda’s formal name] in Kashmir, under the command of Commander Illyas Kashmiri, may Allah preserve him.”

Mr. al-Masri’s message was wrong on several details of the operation, but for investigators, news that elements of al-Qaeda had developed links with jihadi groups acting against India did not surprise anyone.

David Headley, the Pakistani-American Lashkar operative now serving a life term for his role in the 26/11 attacks, had told the NIA of an anti-India “Karachi project” linked to global jihadi groups.

Driven by communal eventsFollowing Pakistani military ruler General Pervez Musharraf’s 2007 siege of jihadists holed up inside Islamabad’s Lal Masjid, Mr. Headley told the NIA, that an ideological war broke out among Pakistan’s jihadis. In spite of efforts by Pakistan’s Inter-Services Intelligence, he said, the “aggression and commitment shown to jihad by the several splinter groups influenced many committed fighters to leave Kashmir-centric outfits and join the Taliban.”

In turn, al-Qaeda became increasingly interested in India, as a means of competing for influence and legitimacy with traditional jihadi groups like the Lashkar, which were supportive of the Pakistani state. In the wake of 26/11, al-Masri himself released a statement warning India of attacks if it struck against Pakistan.

The renewal of a jihadist constituency within India shouldn’t be a surprise: the rise of Mr. Modi, and the Hindu nationalist tendencies he represents, has unleashed existential anxieties among large numbers of Indian Muslims. Though the numbers of jihadi recruits are minuscule, the members of the new cells are also true to a familiar pattern. The earliest Indian jihadist formation, the Tanzim Islahul Muslimeen, was formed to protect Muslims against communal violence, and carried out its first strike, the 1993 bombings of inter-city express trains, to avenge the demolition of the Babri Masjid.

In interrogations, Indian jihad volunteers have repeatedly said they acted to avenge the Gujarat carnage of 2002. Feroze Ghaswala told police he had volunteered to join jihad training after witnessing the mass burial of 40 Gujarat riot victims. Peedical Abdul Shibly and Yahya Kamakutty, both successful computer professionals, are alleged to have prepared to carry out attacks in Bangalore. Men from Kerala trained in the mountains of Jammu and Kashmir with the Lashkar-e-Taiba. Zabiuddin Ansari, from Maharashtra, famously ended up in the 26/11 control room.

Founded in April 1977, SIMI, the fountainhead of the modern Indian jihadist movement, was itself driven by the forces of communal violence. From the outset, scholar Yoginder Sikand has said “that Islam alone was the solution to the problems of not just the Muslims of India, but of all Indians and, indeed, of the whole world.” It drew thousands disillusioned with traditional politics, Dr. Sikand has recorded, providing supporters “a sense of power and agency which they were denied in their actual lives.”

From December 1992, following the demolition of the Babri Masjid, SIMI’s language became increasingly aggressive. In a statement in 1996, it declared that since democracy and secularism had failed to protect Muslims, the sole option was to struggle for the caliphate. Soon after, it put up posters calling on Muslims to follow the path of Mahmood Ghaznavi, the 11th century warlord. In 2001, after the 9/11 attacks, SIMI activists organised demonstrations hailing Osama bin-Laden as a “true mujahid.”

Early in the summer of 2004, a group of young men fed up with SIMI’s inability to act on its own talk gathered in the small coastal town of Bhatkal in Mangalore — and founded what we now call the Indian Mujahideen.

The jihadi traditionTo understand the durability of the jihad within India, it is important to remember that its cadre are inheritors of a long political tradition. In a manifesto sent to the media after their September 2008 bombings in New Delhi, the group said the attacks were carried out “in the memory of two most eminent Mujahids of India: Sayyed Ahmed Shaheed and Shah Ismail Shaheed (may Allah bestow His Mercy upon them) who had raised the glorious banner of Jihad against the disbelievers.” The historian Ayesha Jalal has shown that the notion of jihad was an important theme in both pre-colonial and colonial India. Syed Ahmad and Shah Ismail were killed battling Sikh troops in a failed jihad involving the tribes of Pakistan’s north-west.

Historian Stephen Dale has observed that these ideas stretched to the south of India, noting the work of the Sixteenth Century author, Zayn al-Din al-Ma’bari, who chronicled the jihad against Portugal’s intrusions into the Indian Ocean, hoping to “inspire the Faithful to undertake a jihad against the worshippers of the cross.”

Each bombing the Indian Mujahideen carries out is a medium for a political message enmeshed with India’s dystopic communal landscape: that democratic politics cannot defend India’s Muslims. India’s intelligence and police services deserve credit for the long war they have fought, but it is time for politicians to act to heal our fractured nation