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The Shadow Company made their first appearance in the mission Loose Ends during the third act of the game, under the command of General Shepherd. They appeared as an elite unit of private military contractors stationed in their underground base codenamed "Site Hotel Bravo" somewhere in Afghanistan.
Shepherd became supreme commander of the Shadow Company in his manhunt for a Russian terrorist named Vladimir Makarov and he had given a blank check to use any resources needed. When Shepherd's unit, Task Force 141, was securing intelligence at Makarov's safe house in Georgian-Russian border, the Shadow Company briefly appeared as friendlies to extract TF-141 members Simon "Ghost" Riley and Gary "Roach" Sanderson. However, Shepherd betrayed them by shooting them and secured the DSM before he got his soldiers to dump the bodies in a ditch and set them on fire. Then, he tried to eliminate other TF-141 members John Price and John "Soap" MacTavish, who were looking for Makarov at the vehicle boneyard in Eastern Afghanistan, but the duo managed to avoid his trap by driving their vehicle into their Russian informant Nikolai's C-130 Hercules.
While resided in their command base, it was infiltrated by Price and Soap, who were on a suicide mission to kill Shepherd for his betrayal of Task Force 141. Shepherd, using his new soldiers as bodyguards, asked them to help him escape on a Zodiac. Price destroyed Shepherd's helicopter near the waterfall, and Soap managed to kill Shepherd by throwing a knife through his eye.
The Shadow Company is absent from Modern Warfare 3, however, a container with their logo can be seen.
- They are the first enemy faction in the Call of Duty series to be American.