An acclaimed movie and comic book writer, Goyer's credits include being a co-writer on Christopher Nolan's Dark Knight trilogy and the upcoming Man of Steel reboot.
He previously contributed to Black Ops but only joined halfway through the project, according to Kotaku.
Goyer will write Black Ops 2's story from the ground up, with the aim of creating a "memorable villian" in the form of Raul Menendez, who turns the US and Chinese governments against each other.
Unveiled yesterday, Black Ops 2 is set during a 21st century Cold War and will release on November 13 on Xbox 360, PS3 and PC.
The game's first trailer has revealed that the campaign will feature usable drones and horses, as well as a robot enemy force to fight in a devastated Los Angeles.
Call of Duty: Black Ops 2 multiplayer details were allegedly revealed in a leaked report last month.
> Read our Call of Duty: Black Ops review
Photo gallery - first images of Black Ops 2: