During an ambush attack from Cobra in New York City, Destro plans to blow up the city, including the G.I. Joe Force. Before Destro can though, He, Lady Jaye, Flint, SnakeEyes, & Barbecue get teleported to an alternate world, where Cobra rules the World.
Destro meets the Cobra Commander of that world. the Joes meet G.I. Joe of that world, led by Baroness, LifeLine, Jinx, & Flint & Jaye's Daughter Marissa Faireborn. They are told that many Joes died years ago, they are also told that there Earths are 2 of many infinite worlds in what they call the Many-verse, & were sent to Earth-2 using the M.A.S.S. Device to help them fight Cobra. Lady Jaye feels uneasy of the thought that she & Flint got married & had a daughter, seeing how she was orphan growing up, & never knew her real family. Destro is told by the Commander that G.I. Joe killed their world's Destro. When in reality Cobra Commander killed Destro from learning the truth about Destro's past. Destro soon realizes what the secret is, & finds out the Commander was lying.
Meanwhile on Earth-1, the Joes try to find their friends. Spirit learns from his Shaman GrandFather that they are on a different Earth. During a scuffle with Cobra during the climax, Destro tells Lady Jaye that they are siblings. The Joes soon are able to open the MASS Device and return to their world. A Mid-Credit Scene shows Earth 4 in the Many-verse, the Moon of that Earth revealing the silhouette of NightMare Moon. Scarlett does the PSA.
