Now that the immediate crisis in Mumbai is over, questions and accusations are flying.
Indian authorities are pointing the finger at Pakistan and, whether the allegations prove true, the mere implication that Pakistan is at all connected to the attacks has reignited tensions between the two countries. And that, experts say, could have been the terrorists' true goal.
A senior police Indian police official told Indian media today that the only gunman captured after the deadly attacks claimed to be part of a Pakistani militant group called Lashkar-e-Taiba, whose primary cause is to win the disputed region of Kashmir, which has been a flashpoint in the two countries' relations for more than 60 years.
Indians have long believed this group has been operating as a surrogate for the Pakistani intelligence agency, the ISI. But experts say while there may have been a historical connection, that may no longer be the case.
"These groups, these Kashmiri jihad groups have at times been under Pakistani military control but not necessarily consistently. And they don't necessarily take their orders directly from them," said Bruce Hoffman, a security studies professor and terrorism expert at Georgetown University. "So you could conceivably have a case where some Kashmiri jihadi group turns out to be responsible for Mumbai but has been operating on their own."
Hoffman, who has spent years studying Lashkar-e-Taiba and other Kashmiri militant groups, said they have set their sights much broader than Kashmir and that they think of themselves as part of the larger global jihad against the West.
"Make no mistake, many of these Kashmiri Jihadi groups are as hostile to the U.S. and Israelis as they are to India," Hoffman said, adding that al Qaeda has a history of using groups like these as proxies and could be in some way involved in the Mumbai attacks.
Tom Sanderson, a senior fellow with the Center for Strategic and International Studies in Washington, said that even though it is too early to place blame, one thing is certain: It is virtually impossible for 10 terrorists to have carried out the attacks on their own.
"It was a highly sophisticated and coordinated attack with a large amount of planning," Sanderson said. "That always indicates help from somewhere else."
But the Pakistani government is denying any involvement.
"The state of Pakistan and all branches of the state of Pakistan can say with a great degree of certainty that none of us had anything to do with it," Pakistani Ambassador to U.S. Hussain Haqqani told ABC News. "I don't think it is appropriate to blame Pakistan without any evidence."
A full investigation is already under way. At least six of the more than 180 people killed in the attacks were American and the United States has sent over an investigative team from the FBI to help Indian authorities uncover the motives behind the attack and what -- if any -- larger elements were behind it.
Kashmir a Flashpoint in Indian-Pakistani Relations
Relations between the nuclear neighbors have been volatile since the partition that carved out Pakistan from India in 1947 and triggered the migration of millions of people, as Hindus fled Pakistan and Muslims left India.
Since the beginning, the focus of tension between the two countries has been Kashmir, which despite its large Muslim population was kept within Indian territory. Any flare-up over the mountainous region historically triggers massive military build ups along the Indo-Pakistani border.
The last time that happened was in 2001, after assailants blew up the Indian Parliament in New Delhi. India blamed Pakistani intelligence for the attack, and for the next year, both countries played a dangerous game of chicken along the border.
The standoff drew the attention of the world, because behind the threats and counter-threats were two nuclear arsenals.
But leaders in both countries have taken a more moderate approach in the past couple years and relations between the two countries had been warming.
So in the wake of the Mumbai attacks, Haqqani and other top level Pakistani officials rushed to reaffirm their fragile alliance with India.
"We share the grief of our neighbors," he said. "We know how it feels to be victims of terrorism and Pakistan and India are both victims of terrorism as is the rest of the world. What we see is the need for working together jointly against terrorists and not let the terrorists succeed in driving a wedge between our two countries."
Hoffman said that's exactly what these kind of militant groups are trying to do.
"These kind of attacks are specifically calculated by the terrorists to destroy any sense of moderation; to widen the space between moderates in both countries and at least, if only temporarily, derail any progress towards the resolution of Kashmir," he said.
How does all this affect the United States? Both countries are nuclear powers and key American allies so there are obvious reasons to try to keep peace between them. But Indian-Pakistan relations are also a key factor in the larger "war on terror."
Since 9/11, the United States has given Pakistan more than $5 billion in aid in an effort to stabilize that country and "root out" terrorists operating in the federated territories along the Pakistan-Afghanistan border. A report in the New York Times last year revealed that instead of using that money to fight terrorism, Pakistan used much of it to counter India over the Kashmir issue.
If the Mumbai attacks reignite the distrust between India and Pakistan and bring Kashmir to the fore again, it will not bode well for American counter-terrorism efforts in the region, experts say.
"This could become a major distraction," Sanderson said. "It takes their eye off the ball."
Of course all of this is happening as the United States is trying to make a peaceful transition between presidential administrations. While President-elect Obama had already selected his national security team before the Mumbai attacks, they most certainly underscore the importance of his choices.
As fallout from the Mumbai attacks continues and blame is assigned, Obama and his team will have to add Indian-Pakistani relations to their already long list of foreign policy challenges.
"He has to have a policy even before he assumes office – a policy that is driven by the threat of crisis," Hoffman said.