The leaked footage shows a scene from the first act where the player emerges from an airport lift with several terrorists and opens fire on a crowd of civilians.
Playing as an undercover operative in the terrorist cell, the player must participate in shooting the civilians as they try to escape.
Activision said that the scenes were to "establish evil" but can be skipped.
"The scene establishes the depth of evil and the cold bloodedness of a rogue Russian villain and his unit," the firm said in a statement. "By establishing that evil, it adds to the urgency of the player's mission to stop them.
"Players have the option of skipping over the scene. At the beginning of the game, there are two 'checkpoints' where the player is advised that some people may find an upcoming segment disturbing. These checkpoints can't be disabled."
The statement added that the game will carry an 18 certificate, which will cover "intense, realistic gameplay that mirrors real life conflicts".
Modern Warfare 2 will be released on November 10 for 360, PS3 and PC.