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They planted a secret bug that revealed it was converted into a bomb factory where Ali met others to construct the bombs.
The flat was also used as a location for Ali and others to record suicide videos threatening further attacks against the West.
In his video Ali warned the British public to expect "floods of martyr operations" that would leave body parts scattered in the streets.
Ali was watched as he used public phone boxes, mobile phones and anonymous e-mail accounts to keep in touch with mystery terrorist controllers in Pakistan.
On his arrest, he was found to be carrying an elaborate and damning blueprint for the plot scrawled in a battered pocket diary. Airport security arrangements and details of flights, including the seven highlighted services, were discovered on a computer memory stick in another pocket.
All the defendants except Mr Stewart-Whyte, a Muslim convert, admitted conspiracy to cause a public nuisance and will be sentenced next Monday.
The jury took a total of 54 hours and 11 minutes to reach their verdicts in the retrial.
Ali, wearing a dark blue sweater, showed no emotion as the verdicts were read out, while Hussain nodded his head as the verdicts were read and shrugged his shoulders as he left the secure dock at the back of the court.
Mr Stewart-Whyte looked to the ground as he was cleared before smiling. Afterwards, his lawyer demanded an independent investigation into try him on the basis on "spurious" evidence.
Bernie Duke, one of his solicitors, said: “Mr Stewart-Whyte should never have been charged. We invite the CPS to conduct an independent review into why he was tried when there was in reality only spurious evidence of his guilt and strong evidence of his innocence.”
Judge Mr Justice Henriques thanked the jury for their service over the last six months of the trial and encouraged them to attend the sentencing hearing on Monday.
Speaking after the verdicts, Sue Hemming, Head of the Crown Prosecution Service Counter Terrorism Division, said that the plot would have killed hundreds of people.
“This was a calculated and sophisticated plot to create a terrorist event of global proportions,” she said. “These men wanted to bring down several aircraft in a short space of time, indiscriminately killing hundreds of innocent people - perhaps more - if they'd succeeded in activating their devices while over cities."
Charges in full
Abdulla Ahmed Ali, Assad Sarwar and Tanvir Hussain
Guilty of conspiracy to cause explosions on aircraft, conspiracy to murder, conspiracy to cause explosions and conspiracy to cause public nuisance.
Umar Islam
Guilty of conspiracy to murder; conspiracy to cause a public nuisance. Jury failed to reach a verdict on conspiracy to cause explosions on aircraft.
Ibrahim Savant, Arafat Khan, Waheed Zaman
Guilty of conspiracy to cause a public nuisance. Not Guilty of conspiracy to cause explosions on aircraft. Jury failed to reach verdicts on conspiracy to murder.
Donald Stewart-Whyte
Not guilty of conspiracy to cause explosions on aircraft and conspiracy to murder. Admitted firearms and cannabis possession charge.
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