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.
In "The Enemy of My Enemy," 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.
In "Just Like Old Times," 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 and the murders of Ghost, Roach, Rook and the other TF-141 members. When Shepherd realized that the base was compromised, he asked his new troops to help him escape on a Zodiac while ordering a full evacuation of Site Hotel Bravo and destroying the base in the process, but he still failed to kill Price and Soap.
In the final campaign mission "Endgame," Price and Soap used a Zodiac to pursue Shepherd around the river all the way to the waterfall where Price destroyed Shepherd's helicopter and they dangled down into the river below. After regaining conscious, Soap headed to the helicopter crash site and tried to kill Shepherd, but Shepherd fought back and recalled his reasons why he was doing this after he pinned Soap down and stabbed him with the knife Soap was using. As Price tackled Shepherd away, they fought in hand-to-hand combat until Shepherd gained the upper hand. After Soap woke up, he pulled the knife out of his wound with his last strength and managed to kill Shepherd by expertly throwing a knife through his eye as he looked up.
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