With Pakistan's powerful military breaking with the government and backing a supreme court inquiry into the "memogate" scandal, things do not look good for President Zardari's three-year-old administration.
Former ambassador to the US Husain Haqqani has already lost his job in the row, although he claims he is innocent. Who is to say more heads will not roll?
The scandal revolves around a memo allegedly sent from Pakistan's political leadership via Mr Haqqani to Adm Mike Mullen seeking US help to tame the Pakistani military.
Pakistan's civilian leaders were allegedly worried the military was about to launch a coup after US forces killed Osama Bin Laden in Abbottabad in May.
In recent days, the president's absence from Islamabad has fuelled speculation over what is going on.
Political observers went into overdrive last week when news emerged of his sudden departure to Dubai for medical treatment.
Political pundits think Mr Zardari is waiting outside the country and watching court proceedings from a safe distance. He does not want to get stuck like Mr Haqqani, who is barred by the court from leaving the country until the case is decided, the theory goes.
“Start Quote
End Quote Haroon Rashid BBC NewsDuring the last three years of its rule, Mr Zardari has tried to test waters against the security establishment. The notification to bring ISI under interior ministry a few months after talking over power in 2008 was one such step”
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Conspiracy theories
The existence of the memo is more or less proven. In his court statement, Pakistan's military chief, Gen Ashfaq Pervez Kayani, said the memo's existence had been confirmed by Adm Mullen and Gen James Jones. Now the answer everyone is looking for is - who was really behind it?
President Zardari and Husain Haqani both deny any involvement but the controversy continues to unfold.
The allegations against the ambassador were made by a US-based lobbyist, Mansoor Ijaz, and there are many still unanswered questions about his role. Mr Ijaz has a decade-long association with Mr Haqqani. Is he now playing a double game? Who stands to benefit - the Americans or the Pakistani military?
In his latest submissions, Gen Kayani refuses to name names but he nevertheless does make it clear that it was a conspiracy against the ever-powerful military.
Pakistan's military has defended its right to intervene in politics throughout its existence. No matter how weak it feels, few observers think the army will ever give this up.
Many believe the military must have carried out its own investigations and already reached some conclusions about the memo. But since the matter has now reached the judiciary, the army might be waiting for the names of those responsible to come from judges - it might prefer not to be seen to be weakening another civilian government.
One widely held view is that the conspiracy was actually cooked up by a military which views the Zardari government as having served its purpose. In Pakistani politics nothing is ever totally sure - but the same is true for "conspiracy theories" too.
Others say President Zardari was obediently following the military. People had even started talking about him winning a second term - but "memogate" has now highlighted the underlying split between the country's military and civilian leaders.
During its time in power, the Zardari administration has tried to test the waters against the security establishment. An attempt to bring the ISI under interior ministry control a few months after talking power in 2008 was one such step. Under military pressure, the notification had to be withdrawn within hours.
The appointment of Husain Haqqani, deeply unpopular with the military, as ambassador in Washington raised some senior security officials' eyebrows. "Memogate" - real or concocted - got them his head.
Gen Kayani's submission before the supreme court proves that it was he who asked the prime minister and later the president to recall Mr Haqqani. Again it was the military that made the political leadership take a step they would have loved to avoid. But the real question being asked now is - is this the end of the drama?
'Calm nerves'
It seems President Zardari does not wish to take any chances, even if he is innocent. Official statements have cast doubt on whether he can be sure of his security in Islamabad and implied the medication he was on could be the reason for his illness.
On Friday, Pakistan's main English-language newspaper Dawn urged him to return home to "calm nerves and quell speculation that refuses to die down".
"Like it or not, the reality of Pakistan is that threats to the democratic process do lurk in the shadows. It is the responsibility of the civilian political leadership to deal with those threats effectively," it wrote.
After three years in office plagued by misrule and allegations of corruption, no one is betting at the moment on President Zardari or his government completing their terms.
The days of a military coup are gone in Pakistan, many analysts say, but the going for the government is about to get tougher.
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