G.I. Joe: The Rise of Cobra is based off of the 2009 blockbuster movie, but features a brand new storyline that differs from the movie where an elite group of soldiers must fight against the diabolical Cobra Commander and stop his organization known as Cobra from taking over the world.

The gameplay is similar to Neo Contra with a behind the back view where the player uses a variety of weapons including machine guns and rocket launchers and the Delta 6 Accelerator Suit that makes the player invulnerable for a short period of time. Using these weapons and accessories the player must fight his way through a horde of enemies including soldiers, tanks and jet fighters, along with the standard end of level bosses.

The player can choose from 12 different Joes, but only a certain set at the beginning and unlocking more for completing missions, each with their own weapon and strengths depending upon their rank (Commandos are great at close range, Heavy Weapons are good at shooting from long distances while Soldiers are a mix of both), along with using various vehicles scattered throughout the stages. The game also features a two-player drop-in/drop-out co-op option that allows a friend to join a game at any time, however during gameplay without a human ally, the computer's A.I. will take over for the second on-screen soldier.