Iranian authorities have repeatedly said that Amiri was seized by the CIA during a visit to Saudi Arabia last year, and Iran's state television has broadcast the text of what it said was an interview with him in which he claims he was abducted at gunpoint by US agents while attending the Hajj pilgrimage.
"They gave me a shot which made me unconscious and then transferred me to the US onboard a military plane," Amiri said in Tehran, before making allegations that he was tortured during interrogations in the US.
"Within the first two months, I was subjected to fierce mental and psychological torture by agents and interrogators from the US Central Intelligence Agency."
Speaking to Al Jazeera during his journey back to Iran, Amiri said he had been forced by US authorities to say in a video released on the internet that he was enjoying life in the state of Arizona.
Al Jazeera has not been able to independently verify Amiri's allegations.
'Help of the Saudis'
Amiri said he was "kidnapped with the help of the Saudis" and had been "put under a number of pressures" while held in the US.
He said he had been dropped off at the Iranian interests section of the Pakistan embassy in Washington on Monday after US agents decided they had no more need of him.
|Amiri told Al Jazeera that his alleged abduction was politically motivated [Reuters]
Amiri's disappearance has been linked to rising international pressure over Tehran's controversial nuclear programme, which Iran says is for peaceful purposes but many countries led by the United States say the country is pursuing atomic weapons.
"Behind the scenes this was politically motivated and in my time in the United States where I was held against my will, they asked me for a series of documents ... they wanted to use this as a claim against the Islamic Republic, so they could advance their own political agenda," Amiri told Al Jazeera.
Iran's semi-official Fars news agency, reporting on the case, said that Amiri had been handed over to the Pakistani embassy by US agents, calling it a defeat for US intelligence services.
"Because of Iran's media and intelligence activities, the American government had to back down and hand over Amiri to the embassy on Monday night," Fars said.
The disappearance of Amiri, who worked at a university linked with Iran's Revolutionary Guards, sparked accusations by Iranian officials that he had been kidnapped by the CIA.
Washington has denied the allegations as well as speculation in the US media that Amiri had defected to the US and was working with the CIA.
The speculation was further compounded when a man claiming to be Amiri was shown in two different pieces of video footage on June 7 - one claiming he was kidnapped by US agents and the other saying he was studying in the city of Tucson in Arizona.
These videos were followed by a third a few weeks later in which the man said he had escaped from the custody of US spies in Virginia.
US officials consistently denied Amiri's kidnapping but on Tuesday, PJ Crowley, the state department spokesman, confirmed that Washington had been in touch with him.
"The United States government has maintained contact with him," he said, adding that Amiri "has been here for some time, I'm not going to specify for how long".
Crowley also refused to comment on whether Amiri had provided Washington with intelligence.
But the Washington Post, citing US officials, reported on Thursday that Amiri was paid more than $5m by the CIA to provide information on Iran's nuclear programme.
Shrouded in mystery
Al Jazeera's Alireza Ronaghi, reporting from Tehran after attending a news conference addressed by Amiri, said: "It seems like the Iranians have finally decided to deny the assumption that Mr Amiri had any information that could reveal anything about Iran's nuclear programme to sort of try and lift all the possibilities about Amiri's importance that could probably lead to his defection."
Our correspondent said he had talked to Amiri's wife and even she did not know whether he was alive or dead.
"So no one knew what he has been doing apart from his own claims about what he had been doing and what happened to him," Ronaghi said.
"We have no other source or no other reliable commentary to get a climpse of what he had been doing in the last couple of months, so it is very important for Iranian authorities to get to the bottom of it.
"Iranians have to go through very lengthy sessions with Amiri and that has just started."