The "Memogate" scandal began when Ijaz claimed he delivered a letter approved by Zardari to Mullen that indicated Pakistan's civilian government feared a coup by the military in the turbulent times after the U.S.'s unilateral mission to kill bin Laden on Pakistani soil and sought to remove the threat before the coup had a chance.
In return for the U.S.'s support, the Pakistani government promised to go after the Haqqani terror network in Pakistan, one of the most dangerous groups to U.S. interests in the country, according to the letter, which was first published by Foreign Policy.
Mullen initially did not remember receiving any such memo but was later able to track down a copy, according to Capt. Jack Kirby, Mullen's former spokesperson.
"That said, neither the contents of the memo nor the proof of its existence altered or affected in any way the manner in which Adm. Mullen conducted himself in his relationship with Gen. Kayani and the Pakistani government," Kirby said. "He did not find the memo at all credible and took no note of it then or later."
Once news of the alleged memo spread in Pakistan, so did calls for Haqqani's resignation.
Haqqani has denied any role in writing or delivering the memo and said he is "happy to face an inquiry" about it, according to local reports.
Haqqani took to Twitter after his resignation and said, "I have much to contribute to building a new Pakistan free of bigotry [and] intolerance. [I] will focus energies on that."
ABC News' Luis Martinez contributed to this report.