Pakistani intelligence services revealed in May that a massive manhunt was under way for Amjad Farooqi, alias Amjad Hussain.
Farooqi ran Afghan militant camps, Pakistani intelligence says
The manhunt has now ended with his death in a two-hour gun battle at a house in southern Sindh province.
Farooqi had been linked to suicide bombings, hijackings, the killing of US journalist Daniel Pearl and assassination attempts on Pakistani President Pervez Musharraf.
A 20 million rupee ($330,000) reward was offered for information leading to his capture.
According to Pakistan's Herald magazine, Farooqi was born in Pakistan's Punjab province, part of a refugee family from Indian Punjab.
The magazine says Farooqi became a fundraiser for the now defunct Harkat-ul-Ansar militant group in the mid 1980s.
Reportedly in his early 30s, he fought against Soviet rule in Afghanistan.
Pakistani authorities say it was there he linked with the now ousted Taleban regime, developing close contacts with the top hierarchy of the al-Qaeda network.
The assassination attempt on Musharraf on 14 December
He ran militant training camps, keeping lists of all those who attended, Pakistani security services say.
They believe Farooqi sheltered Khalid Sheikh Mohammad, al-Qaeda's alleged No 3 behind Osama Bin Laden and Ayman al-Zawahri, until Mohammed's capture near Islamabad in March 2003.
Intelligence services said Mohammed was replaced by the Libyan Abu Faraj al-Libbi as head of al-Qaeda's international operational wing, with the help of an Egyptian, Abu Hamza Rabia.
Farooqi then worked with Libbi, who remains at large, on two assassination attempts on President Musharraf on 14 and 25 December last year, intelligence services said.
Media reports said Farooqi had trained air force personnel for the first attack and hired suicide bombers for the second, both in Rawalpindi.
President Musharraf escaped unhurt but at least 14 people were killed in the second attempt.
The BBC's Paul Anderson in Islamabad says Farooqi was also accused of involvement in the attempt to assassinate prime minister-designate Shaukat Aziz in July.
Farooqi was linked to the killing of US journalist Daniel Pearl
At least five people were killed and 25 injured in the attack on Mr Aziz's motorcade in Attock, northern Punjab. Mr Aziz was unhurt.
Intelligence services say Farooqi was also close to Ahmed Omar Saeed Sheikh, the British-born militant convicted of plotting the kidnapping and killing of US journalist Daniel Pearl in Karachi in January 2002.
Farooqi's family said he had been missing since the abduction. The Herald magazine says Farooqi's wife and daughter have been living with her father since then.
Security forces also linked Farooqi to the suicide bombing on the US consulate in Karachi in 2002 that killed 12 Pakistanis.
They believed he was a leader of the Lashkar-e-Jangvi and Jaish-e-Mohammed militant groups,
A leader of Jaish-e-Mohammed, Maulana Masood Azhar, was one of the prisoners India freed in exchange for passengers of a Indian airliner hijacked to Afghanistan in December 1999.
Pakistani security services suspected Farooqi took part in the hijacking.
Residents of Farooqi's home village say he once served as a bodyguard to Mr Masood.