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.
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, 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 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.)