General AustinA U.S. Army Major General who played adviser to the G.I. Joe commanders. Known as "Iron Butt".
- The Brigadier
- No Name Given: His first name is classified.
- Reasonable Authority Figure: He has a thorough understanding of politics that enable him to see viewpoints from all sides.
- Take Up My Sword / You Are in Command Now: After suffering a heart attack, he decided to retire and named Hawk as his successor.
Kwinn the eskimo
An eskimo mercenary who has taken contracts for both Cobra and the Soviets, but sometimes helped the G.I. Joe team due to his sense of honor.
- The Big Guy: A giant of a man with strength to match. He's no dummy, though.
- Exact Words: He promised Dr Venom not to kill him as he lived. When the traitorous doctor shoots him, a grenade falls out of the dead Kwinn's hand, killing Dr Venom.
- Iconic Item: His skull necklace.
- If You Kill Him, You Will Be Just Like Him: Kwinn often compares Dr. Venom to a weasel, but also believes that all men have a "weasel spirit" within. He ultimately decides to let the doctor go to overcome his "inner weasel". This proves fatal.
- Made of Iron: No sells Snake-Eyes in one on one combat, and describes fighting and defeating a polar bear.
- Punch-Clock Villain: Does not particularly like Cobra, really hates the KGB, but takes jobs for both because they pay well.
- Roaring Rampage of Revenge: After Dr. Venom double-crosses him one too many times, Kwinn finally decides to track him down. When it's all said and done, he decides to spare the not-so-good doctor, but see Exact Words above.
- Worthy Opponent: Sees Snake-Eyes as one. Eventually they team up to take down a certain Mad Scientist.
William KesslerThe son of Cobra Commander. Billy was present for his father's Start of Darkness and grew to despise the madman that his father became. He eventually becomes a Ninja Apprentice and occasionally joins forces with others opposed to his father's plans.
- Archnemesis Dad: Cobra Commander.
- Audience Surrogate: Provided a civilian perspective on the Joe vs Cobra conflict.
- An Arm and a Leg: Lost an eye and a leg when Scrap-Iron blew up his car with a missle.
- The Determinator: This put him in a coma for six months, but he did not die.
- The Apprentice: Storm-Shadow is his Obi-Wan, the Blind Master is his Yoda.
- Expy: An Ideal Hero teenager with a pretty common name seeks revenge on a supervillain who wears a Cool Helmet for "what he did to my father." Turns out said villain actually IS his father. Gets trained by a master martial artist. Loses a limb, gains a cybernetic replacement, and becomes a better martial artist. Realizes that his father must be stopped, and that a confrontation with him is inevitable, but does not want to be put in a situation where he's forced to destroy him. Are we talking about Billy or Luke?
- Eyepatch of Power
- First-Name Basis: Usually just called Billy. Kessler is presumably his mother's maiden name.
- La Résistance
- Legacy Character: In "Transformers vs. G.I. Joe" issue 13 he inherits BOTH titles of "Snake Eyes" (from his Sensei) AND Cobra Commander (due to the first Snake Eyes remotely detonating the explosives in the previous Commander's helmet); he wears Snake Eyes' ninja uniform as "Snake Eyes 2.0." while having a COBRA insignia on the uniform's chest to designate him as "Cobra Commander."
- Luke, I Am Your Father: More like Destro telling him "Billy, he IS your father."
- Missing Mom: Cobra Commander told Billy she was dead. He was lying.
- Ninja Pirate Zombie Robot: By the end of "Transformers vs. GI Joe" issue 13, Billy has become a Cobra-G.I. Joe-Transformer-Arashikage-Reptile-human fusion who not only leads the remnants of COBRA as the new Cobra Commander, he has also inherited the Master Sword and the both title and costume of "Snake Eyes." But to show him embracing both roles, there is now a COBRA insignia on the chest.
- Restored My Faith in Humanity: One of the key catalysts in Storm-Shadow's Heel–Face Turn.
- Toyless Toyline Character
The Blind MasterAn American soldier who is blinded by a combat injury and "stranded in Tokyo", and is taken in by the Arashikage Clan, eventually becoming one of their Masters.
- Badass Grandpa: The Marvel comics implies that he war where he lost his sight was Korea, which would put him in his fifties at least.
- Canon Immigrant: Originally a comics only character, but mentioned in the animated movie and actually appears in the live action one.
- Cane Fu: Uses his cane as a weapon.
- Cool Car: A Ford GT 40 Mark V.
- Handicapped Badass: Despite being blind, he's still a master martial artist, is able to sense how close he is to the blast radius of a grenade, and he can still drive ("Only at night").
- Hawaiian-Shirted Tourist: Frequently wore a Hawaiian shirt and a Panama hat.
- Highly Visible Ninja: Hawaiian shirts tend to stand out. Occasionally lampshaded by other characters.
- Made of Iron: "The Blind Master has a talent for surviving explosions."
- Mighty Whitey: He's black, but he is an American who gets trained by a Ninja clan and becomes good enough to actually become one of their leaders.
- Your Eyes Can Deceive You: Teaches this to his students.