In G.I. Joe: Renegades, Cobra Commander (voiced by Charlie Adler) is reinterpreted as a corporate businessman known as Adam DeCobray, head of the legitimate corporation Cobra Industries which masks his terrorist organization. His appearance is similar to his live-action incarnations, save for some details: His lower face is damaged and covered in a plastic shielding wrap. His skin is paler than average humans, and has a red/blue eye and a bald head. He is egotistic, but nowhere as pompous in his promotional speech making as some of his other incarnations nor as personally arrogant. Cobra Commander keeps his disfigured appearance a secret from the world, only ever appearing to the public as a normal-looking human through virtual simulation over video screens, except to the Joes and Baroness, who knew his true self.
Cobra Commander receives a giant cobra from Doctor Mindbender that he calls as Serpentor. During one of Destro's negotiations with Adam DeCobray, Destro's plot to have Doctor Mindbender captured by G.I. Joe is found out causing Cobra Commander to show his true form to Destro. He ends up unleashing Serpentor on Destro, takes control of M.A.R.S. Industries, and places a metal mask on Destro that only Cobra Commander can remove.
The Joes learn of Adam DeCobray's true form when they stole a console at a Cobra Industries Christmas Party. Cobra Commander had to resort to capturing Duke's parents only for them to be rescued by Duke. Cobra Commander sends Baroness to steal back the console on the same military train that Flint is escorting the apprehended G.I. Joe members on.
Eventually, Cobra Commander comes down with an unknown illness, forcing him to wear a mask that covers his entire face in order to breathe properly. He became beyond enraged when Patient X was taken by the Joes, as he plans to use him to create the perfect human/Bio-Viper hybrid as a step towards immortality. Mindbender, however, sees this as an opportunity for Cobra to test out the control chip he implanted in Patient X's head. After tracking down Patient X and the Joes, Cobra Commander mentally orders him to revert into a Bio-Viper and kill the Joes. After Ripcord manages to fight control of the chip and rejoins the Joes, Cobra Commander is less than pleased at Mindbender's failure and sics Serpentor on him. Mindbender convinces Commander that he needs him in order to stay alive. Cobra Commander acknowledges this, then blasts him against the wall and warns him that Patient X must be retrieved alive if the both of them are to survive.
In the two-part finale "Revelations", Cobra Commander makes a bid to revitalize the M.A.S.S. Device. When the Joes invade his mansion, he dons a suit of powered armor, and personally tries to kill Duke, as well as any of the other Joes that get in his way. However, despite his contempt for the idea of ordinary Joes bringing down his empire, his insistence on being recognized as Commander, and his mad dreams of a world remade in his image, Duke manages to knock him into a vat of (acidic) bio-viper fluid in a final struggle as his mansion implodes.
While the Joes triumphantly return to a military base with evidence against Cobra Industries in hand, Cobra Commander crawls out of the remains of his lair, alone, burned and mangled but alive and stating, "They want... to start a war... with Cobra? Then Cobra... will finish it."