The Special Missions series features reserve specialists who are activated as needed, and expands on plots set up in the main title.

One year after the previous series, satellites begin falling out of orbit and crashing into major cities, resulting in massive civilian casualties.

Led by General Joseph Colton, the core roster initially consists of Duke, Flint, Roadblock, Scarlett, Shipwreck, Snake Eyes, Stalker and Storm Shadow.

[1] Thinking that Cobra is responsible for the attacks, General Colton, Duke and Storm Shadow interrogate the Baroness, who is being held in a classified sub-level of The Rock.

[2] Duke, Scarlett and Snake Eyes all leave to conduct solo investigations, while the rest of the team follows a lead to Puerto Rico.

operation,[4] and call in Firewall to help retrofit the VLA in New Mexico, in order to counter the tractor beam that is pulling the satellites out of orbit.

Joe team tracks the signal to Oregon, and discovers that a man named Vance Wingfield, who once attempted to start a nuclear war and was presumed dead, is behind the attacks.

[7] Unable to authorize a rescue mission for Scarlett, General Colton puts the team on leave from active duty.

Naval base in Kyushu, Japan, where Kamakura arrives to discover that Snake Eyes' body is missing.

[11] Meanwhile, the Red Ninja Clan, under the control of Sei-Tin, has stolen Snake Eyes' body in order to resurrect him.

The Joes track the Red Ninjas to China, where Sei-Tin takes control of Snake Eyes, and uses him to exact his revenge against Storm Shadow and Kamakura.

He sends the Joes to Peru, where they take out a Cobra cell and rescue Spirit, who had also been working on a classified mission for Hawk.

Meanwhile, Cobra Commander, who has been rebuilding his forces since the end of the previous series, infiltrates the U.S. government by disguising himself as White House Chief of Staff Garrett Freelowe.

Joe commander, and consisting of Friday (Zarana), Halo (Wild Weasel), High Tide (Copperhead), Mech (Scrap-Iron), and Snake-Eater (Firefly).

[15] Before they arrive, Storm Shadow leaves for parts unknown,[16] but the Phoenix Guard infiltrates The Rock, and manages to capture Roadblock, Shipwreck, Stalker and Hawk.

[17] The remaining Joes fight off the attack, as Duke finally returns, and General Rey discovers the true identities of the Phoenix Guard members.

Dr. Stevens is then revealed to be Cobra hypnotist Crystal Ball, who has brainwashed General Rey, and commands him to kill Duke.

corporation, his Iron Grenadier forces, and his eldest son Alexander to Cobra Commander, in exchange for his and the Baroness' baby.

Joe is warned of a coming "World War III" by Agent Delta, an undercover operative who joined Cobra before the organization's rise.

Cobra bombs Russia, claiming retaliation for the missile attack on Boston, and seizes control of U.S. military installations.

He is partially successful, but Tomax manages to free Major Bludd and several others, while killing those Cobra Commander considered "loose ends".

[27] Cobra Commander and The Plague retreat to a secret base in the Appalachian Mountains, where the final battle takes place.

Scripted by Larry Hama, it centered on the exploits of Storm Shadow, traveling the world as a freelance operative, after leaving the G.I.

The files are presented as computer entries written by Commanding Officer General Joseph R. Colton (the original G.I.

[30] Several other files were later published in individual issues of America's Elite, Special Missions, and trade paper back volumes.