Alternate versions

The extended cut has the following additional material and changes:

• Extended prologue: Mouse and Flint have a contest where whoever can get a hand grenade out from the water barrel with his mouth is the winner. Mouse eventually wins and Flint makes fun of him. Roadblock is annoyed by that and punishes Flint by pushing his head into the barrel again. Duke shows up and makes fun of Roadblock's lecture. While pushing Flint's head again into the barrel, he and Roadblock grin at each other.
• The Blind Master / Jinx / Snake Eyes sequence introduced midway in the theatrical version is now moved to the beginning and its introduction is much more slower, clearer minus the narration. As Jinx prepares to fight Snake Eyes, she is told that to prove worthy of joining the Joes, Snake Eyes must not get a single hair of hers. The fight is longer but Snake eventually wins. She leaves frustrated. The Blind Master gives the indestructible sword to him, telling him to stop Cobra.
• There are more killings shown by the Joes in the base raid and more explicit.
• An additional line by Duke after he lost the shooting contest to Roadblock, looking at his rifle: "Yup, as long as I can bring this."
• The president's son ambushes Zartan with a toy gun. He asks Havoc if he wasn't supposed to protect his father but Zartan instead tells him to clean the chocolate stash in his mother's bedroom. Zartan tells Havoc to "take out his fat ass next time". This scene is also a cross-promotion for Nerf, as the president's son is wielding a Nerf N-Strike Elite Retaliator.
• Extra line by Zartan telling the real president that he's brought back some interns.
• The night helicopter attack is slightly longer.
• The assault on the underground prison by Storm Shadow and Firefly is slightly more graphic. Instead of the original cut, Snake Eyes is surprised by Jinx's appearance who wants to help him, saying she knows where Storm Shadow is likely to go to heal his wounds. He hands her the fighting sticks.
• There's a longer joke of Roadblock and his street friend on his pants.
• Storm Shadow's healing is now shown as one whole sequence.
• Instead of agreeing in the original version, Jaye and Flint are against Roadblock's idea of waiting and killing Zartan in the alley. They want him alive to be brought to Colton.
• Additional graphic shots of Roadblock and Firefly's alley fight.
• As Jaye stitches Roadblock's shoulder, Flint, frustrated comes in and blames Roadblock for not following his own lectures. Frustrated, Roadblock leaves the room to clean the weapons while he sits down. Jaye asks Flint to help her with the dress. There's also a longer reflection of Jaye on the TV screen. Roadblock then comes in again and tells them to help clean the weapons.
• During the collage of the freedom summit, Cobra and his crew leave the boat to meet a small army while Zartan holds his speech.
• In the catacomb assault, Zartan now grabs the case instead of Firefly, thus the order from Cobra has changed with a shot of Firefly with the case removed. Later when he gets the case back, Cobra asks him of the status of the satellites.
• Jinx leads the other presidents through the catacombs while killing a few more Cobra soldiers. She gets pressured into a corner before Snake Eyes comes in for the assist. Meanwhile, Storm Shadow follows Zartan who hides with a soldier. As he enters the room, he hears Zartan's voice saying he never expected him to become a G.I Joe.
• Storm Shadow's fight with the red ninja is longer. Zartan tries to shoot him a few times but misses. Noticing that both fighters buried under the boxes, Zartan tries to shoot him at gunpoint, but instead gets himself at the Shadow's sword point. Then, an explosive firefly lands on the blade and explodes, before Firefly enters the room and retrieves the case.
• More killing of Zartan's guards while rescuing the real President by Colton and Jaye.
• There are extra shots of Roadblock's wielding of the assault gun and the final fight with Firefly.
• Lastly, Jinx wants to return the sword to Snake Eyes but is signaled to keep it, having proving her worth.