Decrypted communications between Indian Mujahideen (IM) and al Qaeda and testimony from suspects have triggered alarm among intelligence officials in New Delhi: the groups appear to be working together to launch major attacks in the region.
The officials told Reuters that plots they had uncovered included the kidnapping of foreigners and turning India into a "Syria and Iraq where violence is continuously happening".
Allegiances between Islamist militant groups can be murky and fleeting, and providing concrete proof of operational ties is notoriously difficult.
But Indian security agencies said evidence they had gathered pointed to growing ties between al Qaeda and IM, a home-grown movement hitherto known for low-level attacks on local targets using relatively crude weapons like pressure cooker bombs.
Weeks after al Qaeda announced the formation of a South Asia wing to strike across the subcontinent, agencies said they had discovered IM members were training with al Qaeda and other groups in Pakistan and Afghanistan for major attacks.
Security officials cite last Sunday's deadly suicide bombing on the Pakistani side of a border crossing with India, and a terror alert on Tuesday at two eastern ports that forced the Indian navy to withdraw two ships, as evidence that militant coordination and activity are on the rise.
"The thing we are looking for is how al Qaeda/ISIS tie up with local groups, especially as the drawdown takes place in Afghanistan," said Sharad Kumar, head of the National Investigation Agency (NIA).
Hardened fighters head home?
ISIS, also known as Islamic State, has carved out swathes of territory in Iraq and Syria, but its influence over militant groups in South Asia is believed to be limited so far.
Al Qaeda is deeply entrenched, however, with leader Ayman al-Zawahri believed to be hiding near the Afghan-Pakistan border and its militants fighting NATO forces in Afghanistan.
Foreign combat troops are due to withdraw at the end of the year.
Some members of IM are already fighting alongside al Qaeda in Afghanistan, according to an Indian government chargesheet against 11 suspected members of the group alleged to have plotted attacks in India.
The worry is that more battle hardened fighters could now turn their sights on their homeland.
Others have enlisted with al Qaeda to try to carry out kidnappings of Jews in India and Nepal to secure the release of Pakistani Aafia Siddiqui, a neuroscientist jailed for 86 years in the United States for attempting to kill US soldiers in Afghanistan.
Siddiqui is a cause-celebre among global militant groups, including Islamic State, which proposed swapping her for American journalist James Foley before executing him when its demands were not met.
IM has also been urged by al Qaeda to open a base in Myanmar to avenge attacks on Rohingya Muslims, said the chargesheet prepared by the NIA, which has gathered hundreds of pieces of evidence of Internet conversations and meetings between militants in India, Pakistan and Afghanistan.
'Itching for action'
The Internet chats, which the United States helped Indian investigators to decipher, reveal tensions between IM and Pakistan's powerful Inter-Services Intelligence agency, which India says has nurtured the group with finance and equipment.
In one conversation, Riaz Bhatkal, one of the founders of IM now based in the Pakistani city of Karachi, tells his men that it was important to build direct ties with al Qaeda, cutting out Pakistan agents whom he described as "dogs".
He talks about visiting al Qaeda leaders in the tribal belt on the Afghan-Pakistan border, despite ISI orders not to do so.
"It has been clear for some time that there is no group that is fully within ISI control. They are all itching for independent action, some want to have a go at us immediately," said an Indian security official.
Pakistani officials deny they have links with the militants. "This is an outdated story. It does not serve any purpose for Pakistan to support such groups," said a senior intelligence official in Islamabad, requesting anonymity as he was not authorised to speak to the media about the issue.
"These terrorists are openly attacking us, the army, innocent civilians, everyone here is a target," he told Reuters. "Why would they do so if we were helping them in any way?"
On Sunday, at least 57 Pakistanis were killed in a suicide bombing at Wagah, which the Tehreek-e-Taliban Pakistan Jamaat Ahrar group, whose leader has ties to al Qaeda, said was also aimed at India.
A spokesperson issued a direct warning to Prime Minister, Narendra Modi, saying his group would avenge the killings of Muslims in Kashmir and Gujarat.
Two Indian naval warships were abruptly ordered back to sea on Tuesday, a day after they docked at Kolkata port after intelligence agencies issued a terror alert.
On Wednesday the warning was widened to the neighbouring Haldia port, the site of a huge petrochemicals complex.
Kolkata Port Trust deputy chairman Manish Jain, who is also in charge of the Haldia port complex, said security had been enhanced several times over in both the ports.
He did not have more details, but a police officer in Kolkata said they had been warned of an attack by Pakistan-based militants.
"It is the Afghan drawdown, there is a competition to do something spectacular. Wagah was the first," the officer said.