The Shadow Company made their first appearance in the mission, Loose Ends, during the third action of the game, under the command of General Shepherd. They appeared as an elite unit of private military contractors stationed in their underground base, "Site Hotel Bravo," somewhere in Afghanistan.
Shepherd became supreme commander of the Shadow Company in his manhunt for Makarov and he had given a blank check to use any resources needed. When Shepherd's special ops unit, Task Force 141, was collecting intelligence at Makarov's safe house in Georgian-Russian border, the Shadow Company briefly appeared as friendlies to extract Simon "Ghost" Riley and Gary "Roach" Sanderson. However, Shepherd betrayed them by shooting them and secured the DSM before his soldiers dumped the bodies in a ditch and set them on fire. Then, he tried to eliminate John Price and John "Soap" MacTavish, who were looking for Makarov at the vehicle boneyard in Eastern Afghanistan, but the duo managed to escape 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.
- The Shadow Company are called "elite", yet they are the easiest enemies to kill.
- When you have the choice to kill or not kill a Shadow Company soldier, it is over 98% to kill them.
- They appear in COD online as a faction pitted against Task Force 141.
- Their logo in COD online is the Tropas logo from Black Ops.
Shadow Company: General Shepherd