Yakub, 28, was the front seat passenger in one of two cars said to be travelling in convoy when four unmarked police vehicles surrounded them at junction 24 of the motorway near Ainley Top in Huddersfield.
The shooting at 6.05pm on January 2 last year was the culmination of an undercover police operation on the day where officers from West Yorkshire had been deployed to keep observations on certain individuals including Mr Yakub, a jury at Leeds Crown Court was told.
Opening the case on Friday, Peter Moulson QC told jurors they would not need to focus on the fatal incident itself.
He said: "We indicate immediately that the case is not concerned with the rights or wrongs of that shooting. That matter is the sole concern of an independent investigation by the Independent Office for Police Conduct (IOPC)
"The case is concerned with the activities, perhaps moreover the intentions, of these defendants on trial who were associated with Mr Yakub before the events of that day.
Mr Moulson said Mr Yakub had been observed in the company of other males in and around the West Yorkshire area on the afternoon of January 2.
The three defendants, Mohsin Amin, 32, Rexhino Arapaj, 28, and David Butlin, 39, were seen to travel from the Cedar Court Hotel in Huddersfield to Cafe de Akbar in Leeds Road, Bradford.
Amin was driving a white Audi A4 with Mr Yakub the passenger, while Butlin drove a white VW Scirocco with Arapaj as his front seat passenger.
Amin and Mr Yakub entered the restaurant - with the Scirocco parked outside - and dined with two men, Mohammed Nisar Khan and Kashif Tahir, for 70 minutes, the court heard.
The prosecutor said Mr Yakub was seen holding a black leather "man bag" as he went in the Cafe de Akbar but Mr Moulson told jurors they may think it was significant that when he exited he still had the bag but was now wearing gloves.
Both the Audi and Scirocco then left Bradford and were travelling together towards Huddersfield when both vehicles were halted by police.
During the stop, a search of the Audi found a Russian Baikal pistol - fully operational and loaded - under the front passenger seat, together with a silencer and a plastic bag of ammunition in the glove compartment.
When the defendants were arrested at the scene it was discovered Butlin had "secreted" a push dagger about his person around his underwear, the jury heard.
Also seized from the vehicles were a number of mobile phones, some of which were encrypted, added the prosecutor.
Mr Moulson said law enforcement agencies were able to download activity from one of the phones which showed a string of WhatsApp messages between Amin and an unidentified man, referred to as Raa, leading up to and on January 2.
He said: "We say that these three defendants were knowing parties to an agreed conspiracy with Yassar Yakub and/or other persons to possess firearms and ammunition.
"And that the weapons were being possessed with the intention of using them if required and the cricrumstances demanded.
"The weapons in that vehicle could not have been for any lawful purpose.
"The messages on Mohsin Amin's phone indicate there could have been possibly a feud and weapons may be used."
All three defendants stated to the police they were unaware of any firearms in the Audi.
Amin, of Broomer Street, Dewsbury; Arapaj, of Thornlea Road, Huddersfield, and Butlin, of Huddersfield Road, Holmfirth, deny conspiracy to possess firearms and ammunition with intent to endanger life.
Butlin also denies having an offensive weapon.
The trial continues on Monday.