If you have an intimate knowledge of the mythos of both Transformers and G.I. Joe, you're gonna get a kick out of finding the various Easter eggs to both franchises.
- Issue 0 begins with a fight between Starscream and Bumblebee that mirrors the battle between the Autobots' ship the Ark and the Decepticons' ship the Nemesis in the G1 cartoon's premiere episode "More Than Meets the Eye, Part 1", with Starscream taking on a vehicle form resembling the Nemesis and Bumblebee riding a spaceship resembling the Ark.
- Duke is depicted as a newcomer to the Joes, a nod to how he was not a part of the team initially in the Marvel Comics continuity.
- Issue 0 has a section focusing on Snake-Eyes titled "Silent Interlude", in reference to the 21st issue of the Marvel Comics G.I. Joe: A Real American Hero comic book that was a dialogue-free Snake-Eyes adventure. It's not completely silent, however, as there are still narration boxes.
- A news ticker in the first issue refers to Cybertron as the "Face of Darkness", alluding to the G1 Transformers cartoon's five-part season three premiere "The Five Faces of Darkness".
- Ravage is the first Decepticon shown speaking in English rather than translated Cybertronian, a nod to how he was the first Decepticon to speak in the Marvel Comics The Transformers comic.
- The second issue has the Autobots and the Joes at one point ride on a road patterend with a grid that has a slightly reddish gradient and folds up to entrap them, resembling the gradient-grid packaging that was used for the original Transformers toys.
- Just before the Constructicons combine into Devastator, Hook tells them to "Merge for the kill", which was an order Megatron gave them in The Transformers: The Movie.
- After Megatron killed Grimlock in Issue #5, he starts wearing Grimlock's T-Rex head over his hand a la the Beast Wars version of Megatron.
- The Joes at one point plan to use a Weather Dominator to make the atmosphere more pleasant. The Weather Dominator originated as Cobra's weapon in the G.I. Joe: A Real American Hero "Revenge of Cobra" miniseries.
- The third issue is titled "Funeral for a Friend", which was also the title of the 26th issue of the Marvel The Transformers comic where Optimus Prime's funeral after his first death in that continuity occurred.
- Decepticobratropolis is shaped like the merged Decepticon/Cobra insignia that was used in the Devil's Due G.I. Joe vs. the Transformers crossover continuity for an alternate cover of the original miniseries' second issue as well as the convention-exclusive preview issue of the second miniseries G.I. Joe vs. the Transformers II.
- Wheeljack communicates through song and speech snippets, much like Bumblebee did in the Transformers Film Series.
- The M.A.S.S. Device is featured, which was used by Cobra in the original 1983 miniseries of the G.I. Joe: A Real American Hero cartoon.
- Zartan is depicted with blue skin, a nod to how his original action figure changed color when exposed to sunlight.
- In issue 5, what appears to be an injured Cobra Commander is unmasked as a Fred (the Freds being a group of Cobra operatives surgically modified to be identical who were prominently featured in the Marvel Comics G.I. Joe continuity), an allusion to how Fred VII impersonated Cobra Commander for a time in the Marvel Comics continuity.
- The sixth issue features an appearance by the Joe Ghostrider, who has his codename provided on his introductory narration box partially obscured as a nod to how the Marvel Comics G.I. Joe continuity couldn't use his codename because of Marvel's concerns of causing confusion with their character Ghost Rider.
- The FCBD Funnies page that is featured in issue 0 of the Transformers: Robots in Disguise (2015) comic has a strip where Cobra Commander states that he "was once a man", referencing his Madness Mantra from being devolved into a snake in G.I. Joe: The Movie, except here it refers to how Cobra Commander was an ordinary schmoe before becoming leader of Cobra.
- In his death throes in the seventh issue, Dr. Mindbender hallucinates being mocked by his heroes, who happen to be infamous historical figures, several of them being most of the ones whose DNA was used to create Serpentor (e.g. Alexander the Great, Attila the Hun, Genghis Khan, Napoleon Bonaparte).
- When Soundwave is resurrected in Issue #10, he starts speaking like his G1 cartoon self. And his resurrection itself is a lot like how he became Soundblaster in Transformers: ★Headmasters.
- Soundwave's resurrection in the tenth issue's backup prose story "Black Cybertron" is assisted by the fallen Autobot Flame in the Cybertronian city of Kalis. This is a nod to the Marvel UK Transformers "City of Fear" story arc, where Flame originated from and created an army of Cybertronian zombies.
- The tenth issue has Tunnel Rat quip "Denial is half the battle", a play on the "And Knowing Is Half the Battle" phrase that was used for the Sunbow G.I. Joe cartoon's PSA segments.
- Blades resembles the original toy of his Transformers: Rescue Bots incarnation, but with the colors of his G1 counterpart.
- The twelfth issue shows Cobra Commander to have killed an interim Cobra Commander, who wears the armor that was used by Cobra Commander in the first season of the DiC Entertainment continuation of the Sunbow cartoon and by Fred VII during his stint as the second Cobra Commander in the Marvel Comics continuity.
- The Baroness's scarring revealed in issue 12 is modeled after magenta spots that appeared on her face in the 44th issue of the Marvel Comics G.I. Joe: A Real American Hero series because of a printing error.
- The final issue's cover depicts Bumblebee and Optimus Prime folding up the American flag, echoing Stalker and Duke doing so on the cover to the final issue of the Marvel Comics G.I. Joe: A Real American Hero comic.
- When Optimus Prime is revived, he comes out of Ultra Magnus and is all white, in reference to the fact that Ultra Magnus is a repaint of the original toy Optimus came from, Powered Convoy, and looked exactly like Optimus without his trailer armor.
- In a Whole Episode Flashback of Destro's origins, Cobra Commander asks Destro if his castle is still haunted by the ghosts of everyone who died at the end of a Destro gun, and Destro assures him that he ghost proofed it.
- Snake Eyes' birth name is revealed at the end of the comic to be Francis Witwicky. "Witwicky" is the surname of several significant human characters in various Transformers continuities.
- The ancient Viking warhammer that both Hawk and Duke carry is in the shape of the logo of the "Adventure Team" rebranding of G.I. Joe from the 1970's.
- The comic features an Eldritch Abomination named Koh-Buru-Lah, the name being a corruption of Cobra-La, an ancient civilization of snake people who were revealed to be the true founders of Cobra in G.I. Joe: The Movie.
- At the end of the series, Megatron takes on a One-Winged Angel form by merging with the Autobots to form Mega-Megatron, who bears a passing resemblance to Megatron's counterpart in the live-action film series.
- The gun Megatron gave Destro in issue 3 is revealed at the end of the series to be a smaller version of Megatron called Mini-Megatron, alluding to how the original Megatron toy had a gun as its alt mode.
- G.I. Joe's HQ the Pit is revealed to have a secret Pit underneath containing a giant alien eyeball, much like in the IDW continuation of the Marvel Comics continuity.
- The page where Optimus Prime returns from the dead is titled "The Return of Optimus Prime" after the two-part episode of the G1 cartoon where Optimus Prime was properly resurrected from his death in The Transformers: The Movie.
- Roadblock is shown to have two daughters at the end of the comic like in G.I. Joe: Retaliation.
- In the Movie Adaptation one-shot, Optimus Prime's actor is identified as O. Ryan Paxton, a play on Orion Pax, which in some continuities was the Autobot leader's name before he became Optimus Prime.
