The tyrannical Megatron, scourge of Cybertron and leader of the Decepticons, currently is deactivated, his head removed and being mocked by Professor Martin. Martin's boss, Dr. Li, reprimands Martin for his antics. A scientific project to harvest Cybertronian technology and utilize it to develop a sentient earth-based peace-keeping weapon shouldn't be taken lightly.

Twelve stories above this secret development facility, the G.I. Joes Hawk, Mainframe, and Firewall prepare for their latest guests: Perceptor, Bumblebee, Grimlock and Arcee. When the Autobots arrive, Perceptor relays a message to Hawk from Optimus Prime; Prime explains that after Shockwave's downfall, Cybertron is enjoying a moment of peace, and as a precautionary measure, the four Autobots have been sent to Earth to prevent Cybertronian technology from falling into the wrong hands.

Roadblock, Snake-Eyes and Scarlett prepare to have one last game of tag in their giant mechs before the Autobots decommission them. Their exercise becomes genuine combat when a giant army of Battle Android Troopers led by Cobra Commander and Zartan attacks the Joes' base. The three Joes fight vigilantly, but are outclassed when Zartan gives the order for the B.A.T.s to combine into the gigantic Cobratron. Luckily, Hawk and the Autobots enter the battle and defeat the metal monstrosity.

Back underground, Zarana (disguised as 'Dr. Wise') communicates with Cobra Commander and reveals the location of the underground bunker by installing a signal beacon.

Bumblebee notices Zartan and the Commander sneaking away from the battle in a Buzz Boar and follows them into the secret development facility. But before Bumblebee can stop the Cobra agents, Zartan incapacitates the small Transformer. With the Autobot no longer a concern, Cobra Commander proceeds to free the scientist's masterpiece: Serpent O.R.

Serpent O.R. awakens and promptly tries to kill the Commander, forcing Zartan to neutralize the creature. Waking up quickly, Serpent O.R. unleashes his tendrils and tosses the three Cobra agents aside.

Above ground, G.I. Joe and the Autobots take care of the rest of Cobra's mechanical army, but then Mainframe contacts them with news of Cobra's entry into the underground facility.

After putting on some fashionable yellow body armor, Serpent O.R. plugs into Soundwave's nearby head and downloads information on the history of Cybertron. After evaluating his objectives, he determines what his goal must be: obtain the Matrix of Leadership.

Featured characters

(Numbers indicate order of appearance.)

Autobots	Decepticons	G.I. Joe	Cobra	Others
Bumblebee (10) Grimlock (11) Arcee (12) Perceptor (13) Optimus Prime (14) Alpha Trion (21)	Megatron (1) Soundwave (2)	Hawk (7) Mainframe (8) Firewall (9) Scarlett (15) Roadblock (16) Snake-Eyes (17)	Zarana (5) Cobra Commander (18) Zartan (19)	Professor Martin (3) Li (4) Serpent O.R. (6) Quintessons (20) Optimus Primal (22)

Notes

Firewall has a TFW2005 coffee mug.
The images in Soundwave's memory are very fascinating. Normally readers wouldn't expect Soundwave to have memory of Unicron or Primal; however, since the G.I. Joe vs. the Transformers crossovers take place in their own continuity, the presence of these figures in Soundwave's memory isn't an error, but rather an indication of a differing history. It's possible that in this continuity, Soundwave has met Primal and Unicron.
Soundwave's history of Cybertron files include:
- The Quintessons building the Transorganics
- The pre-Transformers as gladiator and slave races
- "Mechanoid worlds of junk"
- A-3 becoming Alpha Trion
- Megatron and Soundwave in their War Within bodies.
- Optimus Primal in his original Beast Wars body
- Optimus Prime with the Matrix in his chest
- A portion of Unicron's planet mode
When Hawk and Arcee break apart the last Battle Android Trooper and Hawk gets the bigger part, he says he gets to make a wish. Arcee doesn't get what he means by that. If this is supposed to imply Transformers are unfamiliar with the concept of wishbones, it's a continuity error, since Hook and Scrapper were eager to play wishbone with Doctor Mindbender in G.I. Joe vs. the Transformers #4. Unless it's just Arcee who's unfamiliar.

Covers (4)

Cover A: Bumblebee surrounded by Decepticons by Joe Ng, Espen Grundetjern, and Tom Liu. Combines with the Cover A variant covers for issues 2–5 to form a single image.
Cover B: Bumblebee being beaten by Cobra members (poor Bumblebee) by Tim Seeley and Rob Ruffolo.
Cover C: Giant Optimus Prime (with plenty of Easter eggs) by Don Figueroa and Sunder Raj. Incentive: dealers were only able to order one copy of this cover for every 20 copies of covers A and B ordered.
UDON Exclusive Cover: Autobots and Joes by Joe Ng: Available at Conventions and on the Club Udon website. Combines with Club Udon variant covers for issues 2–5 to form a single image.

Cobra being mean to Bumblebee.
Cobra being even meaner to Bumblebee.
Easter eggs a-plenty.
Udon cover

Snake Eyes Declassified TPB
The Legend of Drizzt Book II: Exile TPB
Dragonlance Chronicles: Autumn Twilight TPB
G.I. Joe Sigma 6 #5
G.I. Joe #10
How to Self-Publish Comics Not Just Create Them vol. 3
Sojourn #1
G.I. Joe America's Elite: The Newest War TPB
Lo-Fi magazine #5
G.I. Joe America's Elite: The Hunt for Cobra Commander
The Art of War #2 (back cover)

Reprints

Other than collections of the full series

Transformers: The Definitive G1 Collection: Volume 96: G.I. Joe vs Transformers, Part 2 (July 15, 2020)

Collects G.I. Joe vs. the Transformers II and the first 2 issues of The Art of War
Bonus material includes a two-page sketchbook containing unused pencil art for the first 8 pages of The Art of War, a cover gallery and an intro by Simon Furman.

Definitive G1 Collection Vol. 96: G.I. Joe vs Transformers, Part 2;
art by E. J. Su/Tim Seeley and Andrew Pepoy (retro art) and Dreamwave (Ramjet)