DUP leader Peter Robinson ordered the emergency session after threatening to resign from his post as First Minister over the revelation that 187 fugitive IRA suspects were sent letters from the government telling them they could return to Northern Ireland without prosecution.
It led to a political crisis and fears the Stormont institutions could collapse - however those concerns receded after Prime Minister David Cameron announced a judge-led inquiry into the letters.
Friday's debate ended with 58 MLAs voting for and 27 MLAs voting against a DUP motion which expressed "grave concern" and "disgust" at what had happened.
It took place after Justice Minister David Ford revealed that he has been told by senior Northern Ireland Office officials that five OTR cases are still being dealt with by the NIO.
Amid angry scenes in the recalled Assembly, Peter Robinson accused former Prime Minister Tony Blair of a "deliberate deception by omission" by not telling most politicians in NI about the deal his government struck with Sinn Féin to deal with on-the-run republicans.
Mr Robinson added: "The answer that there were no plans to legislate and no amnesty would be introduced was a deliberate deception, a deception by omission, for the Government could easily at that stage have indicated that there was an administrative process which included giving letters to OTRs was under way."
Deputy First Minister Martin McGuinness of Sinn Féin - which was the only party to vote against Friday's motion - accused Mr Robinson of being "irresponsible".
He went on: "I am frustrated that the stability of these institutions have been irresponsibly threatened this week and a sense of crisis has replaced the much-needed focus that we needed to get agreement on issues relating to the past.
"Today's recall and motion is about the upcoming election and about the political posturing within unionism. Frankly, I believe the people out there deserve better."
The outcome of the Downey case was morally outrageous and an affront to justice... It was followed by outrage; that outrage was not manufactured or synthetic, it was real.
First Minister Peter Robinson
SDLP leader Alasdair McDonnell said the public must be told about any other secret deals.
He added: "It's impossible to have a proper informed debate on issues that haven't been fully disclosed - we must achieve honesty, openness and transparency around all these issues, starting with rejecting any possibility of secret deals going forward."
Mike Nesbitt, UUP leader, described the letters as a "perversion of justice" and added that his party was ruling itself out of any further Executive talks on the Haass process.
He said: "Let me make clear, for the UUP not only is Haass over but the party leaders (meetings to discuss Haass) is over - and it is over because of Sinn Féin and bad faith."
TUV leader Jim Allister accused Peter Robinson of doing a u-turn over the issue, describing the inquiry as "a farce and a whitewash".
He had said: "If Peter Robinson accepts what the Prime Minister has offered, then, he will have buckled within 24 hours of playing the hard man."
Alliance Party leader David Ford expanded on his earlier comments after he was told that there are potentially five cases, which are understood to have emerged in late 2012, still in the system and under examination.
He told MLAs that it was confirmed that responsibility for these does not rest with the DOJ.
"The position with these five cases is very clear," said Alliance leader Mr Ford.
"After raising the issue both with the Secretary of State and the NIO, I can make it absolutely clear that the five cases in the system - because the NIO put them in the system - remain their responsibility, so this is not a devolved matter.
"The Department of Justice has no part in this scheme, never had any part in this scheme and as long as I am minister will never have any part in this scheme."
First Minister Peter Robinson's threat to quit came this week came after revelations sparked by the collapse of the case against Co Donegal man John Downey, who had been charged over the 1982 Hyde Park bomb which killed four soldiers.
Mr Downey walked free from the Old Bailey because he was sent a letter by the PSNI wrongly telling him that he was not wanted over any crimes - despite an arrest warrant having being issued by the Metropolitan Police.
David Cameron said: "I agree with the First Minister of Northern Ireland that, after the terrible error in the Downey case, it is right to get to the bottom of what happened," Mr Cameron said on Thursday, as he appointed a judge to head up the inquiry.
"The case has already been referred to the Police Ombudsman but, as the First Minister has said, we should have a full, independent examination of the whole operation of this scheme."
The independent, judge-led investigation is to report by May.