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Two popular video games have been ordered removed from store shelves in Pakistan, after shop owners there complained that the games portray their country as an incubator for terrorism.

“Call of Duty: Black Ops II” and “Medal of Honor: Warfighter” are war-themed games where the player gets to shoot enemies and, according to the shop owners, show Pakistan and the country’s prime intelligence agency, the Inter Services Intelligence, as supporting Al Qaeda and jihadi organizations.

The controversial games were removed from shelves countrywide by stores after the All Pakistan CD, DVD, Audio Cassette Traders and Manufacturers Association (APCDACTM) released a notice to boycott both games.

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The circular, written in Urdu, Pakistan’s national language, reads, “The Association has always boycotted these types of films and games. These (games) have been developed against the country’s national unity and sanctity. The games (“Medal of Honor: Warfighter” and “Call of Duty: Black Ops II”) have been developed against Pakistan, and the association has completely banned their sale. Shopkeepers are warned and will be responsible for the consequences if found purchasing or selling these games.”

Dozens of complaints prompted Saleem Memon, president of the APCDACTM in Karachi, to ban the sale of the games and inform its members. Speaking to a foreign news outlet, he said, “The problem is that there are things that are against Pakistan and they have included criticism of our army. They show the country in a very poor light.”

The opening scene of the game “Medal of Honor: Warfighter,” released in November 2012, begins with Task Force Mako, a US Navy SEAL team commissioned to sabotage an Al Qaeda black market arms deal at shipping dock in the southern port city of Karachi, Pakistan. The team plants the explosives on a truck and detonates the bomb, but another explosion destroys the dock, sinking a cargo ship. The plot then reveals a much bigger terrorist threat. From a firefight in the streets of Karachi, followed by a covert mission to investigate Pakistan’s ties with terrorists and PETN, one of the most powerful high explosives known, down to escaping the ISI -- the game centers the story of Pakistan as a jihadi haven.

The game was developed with the help of seven Navy SEAL Team 6 members who were part of Operation Neptune Spear to kill the leader of Al Qaeda.

In Pakistan, speaking about its spy agency and militant groups in the same breath is viewed as taboo and a topic approached with caution. The Bin Laden raid on May 1, 2011, has left the country in utter embarrassment ; many are only gradually coming to terms that the 9/11 mastermind was living just a stone’s throw away from the Pakistan Army’s most notable training academy in Abbottabad. The CIA drone campaign in Pakistan’s lawless tribal belt has killed much of the Al Qaeda leadership and its soldiers, which Pakistan views as infringement of its sovereignty.

A Pakistani security official speaking on the condition of anonymity told Fox News that these games are part of psychological warfare.

He said, “These games are an effort to malign the minds of youth against Pakistan.”

The security official views these games as American attempts to prepare the minds of Pakistanis to accept reports of Pakistan as a failed state, a place that is harboring terrorists, to justify any future action where youth would accept the killing of Pakistanis.

Angered by the CIA’s covert activities, several conflicts between both spy agencies and undeclared foreign intelligence agents in the country, Pakistan clamped down and limited the number of American intelligence officials allowed in the country. The move is further straining relations and leaving the CIA virtually blind on ground intelligence, Fox News has learned.

Regarding the video games, “Not only should the original be banned, but the pirated version sales should be blocked also” strictly speaking, the officer said.

But the games can still be found in stores.

“They are both hot sellers,” said Moeen Ali, owner of Islamabad’s largest game store. He wasn’t aware of the ban, but told Fox News that more than 5,000 copies of “Call of Duty: Black Ops II” had been sold in Pakistan since its release.

The number of copies sold does not account for the unprecedented quantity of pirated copies available for just under $2 available in Pakistan.

“’Medal of Honor’ would be around the same. My store has probably sold up to 1,000 copies,” says Ali.

November 2012’s highest grossing game of the month, “Call of Duty: Black Ops II” focuses on Nicaraguan narc-terrorist Raul Menendez and contains a mission in Pakistan to get intelligence on the villain.

“It’s not the first time a game has been banned or boycotted here,” says Ali. “’Assassin’s Creed’ was banned in Pakistan because Muslims found content offensive and I stopped selling it.”