The revelation that Nisman had not just accused Fernandez of covering up Iran's role in the bombing, but drafted an arrest warrant for her, is likely to fan the flames of the conspiracy theories that have abounded since his death.
The draft was dated June 2014, indicating that the prosecutor had considered seeking an arrest warrant for some time, but in the end, filed a criminal complaint that did not include this petition.
The draft document calling for the President's arrest was found in a trash can in Nisman's apartment, lead investigator Viviana Fein said. The document also called for the arrests of Foreign Minister Hector Timerman and several political supporters of the President.
The existence of the draft arrest affidavit was first brought to light by the Argentine newspaper Clarin. On Sunday, the paper published its story, including images of the document.
The government called Clarin's report "garbage."
Affidavit warns of pressure on judicial system
Fernandez's Cabinet chief, Jorge Capitanich, ripped up a copy of the offending article during a news conference. And Fein, the lead investigator in Nisman's death, also reportedly denied that such an arrest affidavit existed.
On Tuesday, however, Fein released a statement saying that there had been a miscommunication. She admitted the document existed and that it was included among the many documents gathered by police from Nisman's apartment. All the documents are awaiting analysis, she said.
The draft affidavit warns the would-be judge that Fernandez, Timerman and the other subjects of his complaint could exert pressure on the judicial system, Clarin reported. Those he accuses, Nisman wrote, have a "total lack of scruples."
Fernandez, who is on a trip to China, did not immediately make any public comments on the matter.
Whatever Nisman may have contemplated, he never filed for arrest warrants, the state-run Telam news agency noted.
State media also highlighted Fein's comments that her initial denial of the existence of the draft documents was the result of a clerical error, and not any government pressure.
Debate on new spy agency begins
Debate began Wednesday in Argentina's Senate on legislation supported by the President to dissolve the country's domestic intelligence service.
The government has alleged that a former intelligence chief fed false information to Nisman and may have had a role in his death.
If passed, the bill would dissolve the Secretariat of Intelligence (SI) and replace it with the new Federal Intelligence Agency.
Fernandez proposed the bill, saying that the service has "not served the interests of the country."
The bill also proposes transferring control of phone tapping from the intelligence agency to the public ministry.
The Senate vote on the measure is slated for February 11. It will then go to the lower chamber of Congress. Supporters hope to have it signed off by the President by February 25.
What really happened?
Nisman, 51, was found dead on January 18. A gun and shell casing by his body made it appear to be a suicide, but suspicions were confirmed when a test found no gunpowder residue on his hands, as would be expected if he had pulled the trigger.
Fein said on Tuesday that a second test for gunpowder would be carried out to confirm the result.
For 10 years, Nisman had been investigating the deadliest terrorist attack in Argentina's history: the 1994 bombing of a Jewish community center that left 85 dead and hundreds wounded.
Nisman's body was found inside the bathroom in his luxury 13th-floor apartment in a swank Buenos Aires neighborhood. He had a 10-man security team guarding him, but he reportedly dismissed them only hours before his body was discovered.
The night before Nisman died, he spoke with opposition congresswoman Patricia Bullrich. Nisman was preparing to present his shocking report before the congressional committee that Bullrich chairs, and he asked about his safety.
"He said, 'Are you going to guarantee my security'?" Bullrich recalled. Yes, she told him.
Fifteen hours later, Nisman was dead.
Massive cover-up of bombing alleged
Nisman's nearly 300-page report pointed to an alleged massive cover-up of who was behind the 1994 bombing. Arrest warrants were issued in 2006 for eight Iranian nationals believed responsible for the attack.
But in his report, Nisman claimed that Fernandez's government helped orchestrate a bargain with Iran: Cash-strapped Argentina would get Iranian oil. Iran would get Argentine grain and meat. And the bombing would remain unsolved.
"The most important information in the investigation (by) Nisman is the Argentine government (wants) to take away (Iran's responsibility in) the bombing of AMIA," Bullrich said. "They want to destroy the investigation of the Argentine justice."
The target of the bombing was the Argentine Israelite Mutual Association, known as AMIA.
A .22-caliber pistol was found by Nisman's body. Investigators said the DNA found on both the gun and Nisman's clothing was from him alone.
Diego Lagomarsino, a former aide to Nisman, told reporters that he had given Nisman the gun. Why? He said Nisman asked for the gun because his daughters had become afraid of his security team.
Fernandez took to Facebook to first call the prosecutor's death a suicide. A few days later, she changed her mind. In a posting, the President said she now believed that Nisman had, in fact, been murdered but it was actually a plot against her -- to kill the prosecutor who was on the verge of disclosing potentially damaging and false information about her.
In other words, she said Nisman was killed to make her look guilty.
Fernandez said all of this from behind closed doors. But a week after Nisman's body was found, she appeared on national television. Dressed in a white pantsuit and speaking from a wheelchair because she had suffered a broken ankle, she called for the dissolution of Argentina's intelligence service
, believing the spy service was trying to incriminate her in Nisman's death.
She told the nation that "groups of prosecutors, groups of judges, anonymous informers and also journalists" were all out to destroy her.
Capitanich, the Cabinet chief, told CNN and other media outlets that Nisman's allegation is "crazy, absurd, illogical, irrational, ridiculous, unconstitutional."
A special poll by the firm Ipsos showed nearly 70% of those surveyed believed Nisman in fact was murdered. The poll backs Bullrich's observations.
"In Argentina, Argentina thinks that the prosecutor Nisman ha[s] been killed ... nobody believe about the hypothesis about the suicide, nobody," Bullrich said.
Ten days after Nisman's death, he was buried in a ceremony carried live on Argentinian television. His grave is in the same cemetery where victims of the 1994 explosion are buried.