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Westminster Magistrates’ Court heard that he has also been charged with preparing acts of terrorism between May 2019 and September this year, with previous plans to kill other members of parliament.
The court heard that he travelled to Sir David’s constituency surgery, at Belfairs Methodist Church, by train from his home in Kentish Town, London.
Mr Ali had made an appointment to see the Conservative politician at 12pm, and allegedly stabbed Sir David after being taken to meet him by an assistant.
The victim received medical treatment at the scene, but was pronounced dead at 1.10pm.
A post-mortem found the cause of his death to be multiple stab wounds to the chest, the court heard.
Mr Ali, wearing a grey tracksuit and thick-rimmed black glasses, spoke only to confirm his name, age and address during the hearing.
He was remanded in custody ahead of a hearing at the Old Bailey on Friday.
Sir David, 69, was one of Britain’s longest-serving MPs and was married with five children.
Announcing the charges against Mr Ali earlier on Thursday, Nick Price of the Crown Prosecution Service said: “We will submit to the court that this murder has a terrorist connection, namely that it had both religious and ideological motivations.”
Matt Jukes, the head of UK Counter Terrorism Policing, said officers had been working with the government and parliamentary authorities to review security measures.
“Police forces across the country have been working with individual MPs to review their specific arrangements,” he added.
On Monday, parliament paid tribute to Sir David as it was announced that Southend would be granted city status, in recognition of his decades-long campaign for the seaside town to be given the honour.