Judge Claudio Bonadio asked lawmakers to remove Fernandez's immunity from arrest, which she gained upon being elected senator. She was sworn in last week. While Fernandez, who was president from 2007 to 2015, faces several other court actions, it's the first time a judge has requested her arrest.
Several aides and allies of Fernandez, including former Legal and Technical Secretary Carlos Zannini and activist Luis D'Elia, were arrested Thursday on the same charges. The judge ordered former Foreign Minister Hector Timerman to be held under house arrest due to health issues.
Fernandez, known for fiery speeches that blast rivals, said Bonadio and President Mauricio Macri represented a "political and judicial organization to persecute the opposition."
"This whole thing has been invented on the basis of things that didn't happen," she said.
Prosecutor Eduardo Taiano said the charge of treason carries a potential prison sentence of 10 to 25 years while aggravated cover-up has a six-year penalty.
The judge is backing an assertion by former prosecutor Alberto Nisman that a 2013 agreement with Iran, which was portrayed as a joint attempt to solve the case, in reality ensured that the Iranians involved would never be prosecuted. The deal was approved by Congress, but was later declared unconstitutional by the courts.
For Fernandez to be arrested, two thirds of the Senate would have to vote to remove her immunity. It's unclear whether the Senate would move against Fernandez, who is still popular with many Argentines despite mounting legal woes. The Senate usually avoids votes to allow the arrest of colleagues until they have been found guilty.
Even if Fernandez retains immunity, the judge could continue investigating because the protection is only from arrest. Fernandez and the other defendants have several options to appeal, which could drag the case out for years.
Fernandez is not only former president-turned-senator to face such charges. Carlos Menem, president between 1989 and 1999, was convicted of arms smuggling in 2013 and has been charged or investigated in several other cases of wrongdoing, including an alleged cover-up in the Jewish center bombing. Immunity thanks to his Senate seat has kept him from incarceration.
Fernandez and the other defendants have repeatedly denied wrongdoing or involvement in any cover-up involving Argentina's worst terror attack, the 1994 bombing of the Argentine Israelite Mutual Association center in Buenos Aires, which killed 85 people and wounded hundreds. Investigators have linked former Iranian officials to the attack, but Iran has denied any connection with the attack and declined to turn over suspects.
Courts initially rejected Nisman's indictment, but Argentina's top criminal court last year accepted a request by a coalition of Jewish associations to re-examine the charge against Fernandez, Timerman and other officials originally made by Nisman on Jan. 14, 2015.
The case took an even more sinister turn when Nisman was found dead with a gunshot to the head four days later.
The initial police reports and autopsies found no sign anyone else had been present when Nisman died, and federal police said the prosecutor shot himself.
But Taiano said in November that a re-examination of the evidence showed that Nisman was murdered.
The judge also ordered the arrest of Argentine Jorge Khalil, a Muslim businessman, and leftist activist Fernando Esteche. Both were detained on Thursday.
Bonadio also charged intelligence chief Oscar Parrilli, former Treasury Prosecutor Angelina Abbona and several other former officials, but said they could remain free.
An earlier version of this story said the judge's request was to remove immunity from prosecution. It is to remove immunity from arrest. The possible sentence for treason is 25, not 15 years.
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