What's cooking up in Karachi? The seizure of one of the biggest caches of arms and ammunition from a small house in Azizabad on Wednesday has stunned the city.

If all this is true and alleged MQM militants with knowledge of leadership are involved, it may further tarnish the image of the party, not internally but also internationally. At the same time if police and agencies cannot establish the case, it would raise some serious questions about 'Karachi Targeted Action' (KTA).

Both factions of MQM, Pakistan and London, have denied their involvement in it, but investigators are convinced that it not only belongs to MQM, when it was united, but they have also prepared a list of their leaders who would be looking after Nine-Zero and Khursheed Memorial Hall in between 2013 and 2015. These may also include some from Pak Sarzameen Party (PSP) as well.

It is such a huge consignment of a highly sensitive nature that security officials fear the involvement of foreign intelligence agencies including RAW.

Three questions are of utmost importance here:

(1) During which period were these arms and ammunition brought?

(2) How were they brought?

(3) Why were they brought and dumped? As it was not merely for street crime or target-killing

Politically too, it has coincided with an important video message of MQM founder Altaf Hussain, which indicates that MQM-London will be getting active after Muharram, with the announcement of a small Rabita Committee comprising 12 to 15 people. It is also a test of his strength after August 22, as well as bigger challenges for MQM-Pakistan.

But the message has also 'alerted' security agencies which fear the possibility of a new wave of 'violence' and believe that if more arms depots of such magnitude or even smaller are found in the city or even in other urban centres, the operation is far from over.

What happened to the weapons recovered last year and the alleged documents which contained details of militants and arms and ammunition? Where in the city have all these weapons been dumped?

No one can deny the importance of the biggest achievement of Karachi police since KTA was launched in September 2013, and it is also true that it may take a few weeks or even a month or two before police submit a report in the court. The quality and quantity of arms and ammunition as claimed by the police indicate that it could be part of a much deeper conspiracy against the economic and commercial hub of Pakistan.

As some officials feared, it looked like an arms depot of a 'private army' and certainly required army commando-like expertise to use some of these weapons. If some of it belongs to NATO, one cannot rule out the possibility of 'inspection from NATO' or US and British intelligence visiting the city to verify them or at least seeking reports from their Pakistani counterparts.

Earlier, when Rangers had raided MQM's Khursheed Memorial Hall in March 2015 and claimed recovery of some of the weapons used by NATO, the top NATO official had denied it.

Three months prior to this raid, DG Rangers Major General Bilal Akbar in a meeting with MQM Rabita Committee at Governor's House alerted them about certain houses of Azizabad being used as hideouts of alleged militants and involvement of Indian 'RAW'.

Once again such a claim has been made, this time by the police and that too at a time when the Chairman of NATO Military Committee General Petr Pavel during his visit to Islamabad met the Prime Minister Nawaz Sharif on Thursday.

This probe would certainly expand after the formation of Joint Investigation Team (JIT), but police have already acquired the services of the army for highly sensitive forensic tests of very sophisticated weapons.

It would also be interesting to find out whether any of these weapons have also been used in any terrorist or criminal activities as yet or had just been dumped and yet unused.

If more such 'arms depots' were found in Azizabad or in any part of the city, as indicated by the police and even senior Rangers officials to me, the Karachities were sitting on a 'volcano,' as it also includes weapons to hit aircraft and ships as they are certainly not meant for mere control of areas or target killings. They are also trying to determine the total cost of these consignments but fear that it may run into millions. One senior officer said "it could be around 600 million or maybe more".

But the question, which even Sindh Chief Minister Syed Murad Ali Shah has asked from IGP Sindh, Mr AD Khawaja is "how these weapons reached Azizabad and without anyone's knowledge", an unimpeachable source in the CM House disclosed to me.

The source said Mr Shah still wants a complete presentation and asked the police chief to "fully satisfy him" about some of the unanswered questions which have been raised about this unprecedented seizure, perhaps among the biggest in the country.

Police and Rangers officials now convinced that these weapons were dumped after March 2015, following Rangers raid at Khursheed Memorial Hall, from where it had not only recovered huge weapons including 'licences arms', but also arrested some suspects.

"Many of these weapons had been found covered in newspapers of mid-2015, which I personally believe could have been shifted after the raid in a bid to protect them," said a senior Rangers official.

Some of the houses around Nine-Zero, Azizabad, the residence of Altaf Hussain and the strongest constituency of MQM, had been under 'intelligence surveillance' before and after the March 2015 raid. How come police and other intelligence agencies remained unaware of it? Had there been any 'intelligence report' about any such activities during all this period.

Intelligence agencies had even collected important evidences from the same locality in Dr Imran Farooq's murder case and had even traced one of the 'missing laptops' of a foreign intelligence official within few days.

Ironically, the story of the 19,000 missing NATO containers had never been properly probed after the inquiry commission, constituted by the Supreme Court and headed by former IGP Dr Shoaib Suddle, confirmed the presence of weapons in some of these containers. In the light of his report, some officials were also arrested and the case is still pending before a customs court.

It also raised a question as to whether NATO had made any 'insurance claims' over the missing containers as they were all 'insured'.

Therefore, the JIT which will be comprising officials from the premier intelligence agencies have a tough task ahead of them as it is not a simple 'criminal case' and may turn out to be a case of national security.

The Karachi operation has lot to do with the 2011 'Karachi bey ammni case', and credit to this goes to former Chief Justice of Pakistan Mr Justice Iftikhar Muhammad Chaudhry, who took suo-moto of the deteriorating law and order situation in the city.

During a few of the proceedings in Karachi, also witnessed by me, the former CJP raised very specific questions about the supply of weapons to Karachi from different routes including land and sea.

"If these arms and ammunitions come in containers after passing through hundreds of check posts, who is responsible? Similarly, if it comes through ships, why has it never been caught at the security gates?" he asked from senior officials of concerned agencies.

Thus, the Azizabad arms case requires a lot of questions from former Home Minister Anwar Sial, and former IGP Sindh Anwar Zaheer Jamali, who is already facing some serious inquiries, and also local commanders of premier intelligence agencies.

Will the JIT, through an independent, transparent, and impartial probe, be able to unearth this huge conspiracy to hit Pakistan's economic hub and get to the bottom of the presence of unofficial 'arms depot'? Or will it turn out to be merely a case for 'media hype'?

How did the weapons come? From where did they come? And which of the officials were either silent or part of the conspiracy? If the JIT manages to prove and get all those responsible, the case can have international consequences as well about what has been going on in the city of 20 million.

The writer is the senior columnist and analyst of GEO, The News and Jang.