The Red Shadows are the remnants of the Arashikage ninja clan, the world's greatest assassins. Led by the ninja known only as Storm Shadow, they have allied themselves with Doctor X, who has enhanced their abilities with mechanical and biological augmentations.
When Mercy Gale was revealed as Doctor X, Storm Shadow and her Red Shadows rendezvoused with her on an airship. Though the airship was destroyed by the forces of the Action Man Programme, no bodies were found in the wreckage. When Joe Colton recruited X into the Iron Ring, he promised to use the Talisman to upgrade the cybernetic limbs of the Red Shadows and grant them Dire Wraith-traits. The Red Shadows were promised further upgrades once Cybertron had been conquered.
A group of Red Shadows ninja were confronted by G.I. Joe in Tokyo while stealing supplies for the Section Sabine moonbase. Though the ninja outnumbered the Joes, and were able to resist the Joes' weapons with their mechanical enhancements, they were convinced to stand down by the Joe team's secret weapon: the former Decepticon Skywarp.
When Action Man was accidentally brought to Section Sabine, Storm Shadow and the Red Shadows were present; when he escaped into the base, he killed one of the pursuing ninja. When Kup broke into the base, several Red Shadows were pulled out by the explosive decompression, and though some of those remaining used their Wraith-like enhancements to fight off Mayday, Garrison Blackrock, and the Micronauts, they ended up evacuating the base using the M.A.S.S. Device when the Ore-13 was destabilized.
The Red Shadows joined in the attack on the Onyx tower in Buenos Aires to retrieve the Talisman. A large number of them managed to down Skywarp while Mayday used another to repel down to the tower's lower levels. The surviving Red Shadows escaped back to the Iron Castle and bore witness to Joe Colton's declaration that it was time to take the fight to Cybertron.
During Earth's induction into the Council of Worlds, the Red Shadows concealed themselves within hollow Cybertronians to act as Trojan horses. When the signal came, the Red Shadows engaged both G.I. Joe and the Cybertronian Security Force. Their Wraith aspects were detected by the Solstar Order who placed Cybertron under quarantine as a result. Ironhide simply rammed a large number to death while Soundwave used his powers to overload their minds.
As the command staff of the Iron Ring made their way deeper into the bowels of Metroplex, Colton set up a trap of Red Shadows which was triggered by Sunstreaker's group. Sunstreaker managed to best the Shadows only to be shot into stasis by Colton. Another Red Shadow trap was set up in Cybertron's underground and was triggered by Optimus Prime and Scarlett's group who defeated them.
- The Red Shadows are based on the villains of the Action Force franchise, the UK equivalent of G.I. Joe: A Real American Hero. Rather than ninjas, those baddies were a paramilitary force who eventually became Cobra; they were led by Baron Ironblood, which doesn't seem to be the case in IDW. (Also, they had reptile-men called Krakens and a skeleton man called Skeletron, which is awesome.)