Perez Molina formally stepped down Thursday and a prosecutor ordered him jailed without bail hours later, as Guatemala's political crisis came to a dramatic climax.
Vice President Alejandro Maldonado was sworn in hours later as the country's new leader. Maldonado promised to lead an honest and inclusive transition government, and to restore Guatemalans' confidence in their democracy.
He will serve the rest of Perez Molina's term, which ends in January. The country is set to vote Sunday for the next president in an election whose timing has nothing to do with the crisis.
The former leader on Friday denied prosecutors' allegations that he was involved in a conspiracy to defraud the state by letting businesses evade import duties in exchange for millions of dollars in bribes.
"The first thing I want to deny, I don't belong to 'La Linea,'" Perez Molina said, referring to the name of the fraud scheme, Spanish for "The Line."
The hearing wrapped up in the afternoon, and Judge Miguel Angel Galvez said he would make a ruling Tuesday on whether to order a trial. Perez Molina was ordered to remain in custody until then at the same military barracks where he spent his first night as an ex-president.
Prosecutors argued that Perez Molina was aware of the conspiracy, and formally asked the judge for a trial on charges of illicit association and graft.
They presented 77 wiretap conversations totaling more than five hours and recorded over multiple days, as well as photographs and seized documents that detailed how the bribes were divvied up.
More than 20 other officials, including the president of the central bank, have been arrested over the alleged scam, though how much money was involved is still unclear.
Prosecutors and a powerful U.N.-backed anti-corruption body known as the CICIG moved against Perez Molina following months of investigations and findings taken from some 89,000 telephone taps, almost 6,000 emails and 17 raids.
Former Vice President Roxana Baldetti resigned on May 8 after her former private secretary, who remains a fugitive, was named as the alleged ringleader of the scheme. Baldetti, now jailed and facing charges, also says she is innocent.
One recording played twice for the court was of two voices said to be Baldetti and Salvador Estuardo Gonzalez, the alleged financier of the ring, who has also been jailed. Prosecutors argued that it was evidence of a hierarchical relationship between the two, and that they discussed "numbers" and "payments."
Prosecutors alleged that Perez Molina knew about the scheme, cooperated to allow it to operate and received a percentage of the illicit proceeds. They also showed a photo of Gonzalez with Perez Molina.
Defense lawyer Cesar Calderon invoked a restaurant metaphor to argue that the state's case was weak.
"I was left waiting for the main course ... of their investigation," Calderon said.
"Your honor, I am not going to risk my dignity, my work, nor all the effort I have made for Guatemala in return for $800,000," Perez Molina said in allusion to dollar figures presented by prosecutors.
Dressed in a sharp blue suit and striped tie, Perez Molina addressed reporters as the hearing concluded and before he returned to the military base. He expressed regret about his legal situation and that the political drama was playing out on the eve of elections.
"Personally I am very saddened," he said.
Earlier he told The Associated Press he had been uncomfortable and slept little the previous night, and hoped to be granted bond or house arrest.
"No jail is good. ... I hope the judge gives me an alternative," Perez Molina said.
Al Jazeera and wire services
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