The original incarnation of the group included five MCs: Vinnie Paz, Chief Kamachi, Esoteric, Virtuoso and Bahamadia, along with Jedi Mind Tricks producer Stoupe the Enemy of Mankind and producer/DJ 7L (of 7L and Esoteric fame). The group released their debut EP/single "The Five Perfect Exertions" b/w "War Ensemble" in 1998. Both tracks were later included on JMT's 2000 album Violent by Design; with "The Five Perfect Exertions" being remixed into "Exertions Remix", and both "Exertions" and "War Ensemble" shedding Chief Kamachi's appearance. The Army of the Pharaohs project was put on the back-burner while JMT's career took off.
The group wouldn't return until 2005 without Virtuoso and Bahamadia. The group was now composed of Paz, Kamachi, 7L & Esoteric, Outerspace, Apathy, Celph Titled, Reef the Lost Cauze, Des Devious, Faez One and King Syze. After years of anticipation, the group recorded their debut album, The Torture Papers. It was released in March 2006 on Babygrande Records. The album was produced by AOTP affiliates such as DC the MIDI Alien, Undefined, Beyonder, Loptimist, and German producer Shuko. The album featured the single "Tear It Down" b/w "Battle Cry", the former featuring a music video, and the latter was a posse cut featuring nine of the group's then ten members. The album debuted in the top 50 on Billboard's Top Independent Album chart, and hit #42 on the magazine's Heatseekers chart. An unofficial continuation of The Torture Papers soon began circulating around the internet called The Bonus Papers. It was composed of tracks not released on the album.
The group's second album, titled Ritual of Battle, was released on September 25, 2007. Ritual of Battle's single, Bloody Tears, featured a sample borrowed from the soundtrack of the video game series Castlevania. The group added four new members for the album: Jedi Mind Tricks member Jus Allah, Doap Nixon, Demoz and King Magnetic. Apathy was not featured on Ritual of Battle as he was working on solo projects.
On May 17, 2009, Apathy mentioned on his Myspace blog a new AOTP album was completely finished. The album was titled The Unholy Terror and was released on March 30, 2010. This album marked the return of Apathy and the addition of new AOTP members: Block McCloud and Journalist. Two songs, "Godzilla" and "Contra Mantra", were released before the album. This album also marked the departure of Chief Kamachi who left the group because of business issues.
There are rumors about a fourth album, named Heart of Darkness, for a summer 2011 release. Producers will include Sicknature, Snowgoons, Ill Bill, Celph Titled and Stoupe, the original AOTP producer. An unreleased, untitled track featuring Canibus, former AOTP member Virtuoso, R.A. the Rugged Man and Sabac Red produced by Stoupe will be on this album.