• Commentary by Director Jon M. Chu and Producer Lorenzo di Bonaventura
• G.I. Joe: Declassified - HD (Mission Briefing - HD / Deployment - HD / Two Ninjas - HD / The Desert Attack - HD / Cobra Strikes - HD / The Lone Soldiers - HD / The Monastery - HD / Fort Sumter - HD)
• Deleted Scenes - HD (Pakistani President Assassinated / Interns / Arlington)

Framed for crimes against the country, the G.I. Joe team is terminated by the President's order, and the surviving team members face off against Zartan, his accomplices, and the world leaders he has under his influence.