The Battletoads comic appeared in issue 25 of Nintendo Power magazine in June 1991, and was written by Rare employee Guy Miller. It is generally considered the canon backstory of the series, since it is partially referenced in Battletoads in Battlemaniacs
The first half of the comic focuses on the origins of the Battletoads. The story begins at the Psicone Corporation, where three game testers named Morgan Ziegler, Dave Shar, and George Pie are demonstrating the company's newest video game, Battletoads, which uses advanced virtual reality technology to allow the trio to be the 'Toads and control them directly. As the demo ends, the trio are confronted by Psicone General Executive Alexei Vakuse, as well as chief technician Silas Volkmire. Vakuse proposes to the trio and Volkmire that Psicone wants to tweak the difficulty of the Games Generator, so as to lure in more fans. Although Vakuse tells Volkmire when he means "tweak" he means slightly alter the difficulty, as the Battletoads are Psicones's biggest meal ticket. However, Volkmire has other ideas, and sees Vakuse's authorization as something more nefarious.
In Volkmire's pad, while the technician is working on some code, he enters some commands and brings the Dark Queen into his home. Supposedly only being computer code, the Dark Queen cryptically hints that she is not Volkmire's creation. However, she does agree to aid him on account of their shared enemies: the Battletoads.
Meanwhile, Morgan, Dave, and George find themselves unable to relax. Their thoughts are on Vakuse and Volkmire, and how they can't seem to trust either of them. Deciding to see what they're up to, the trio breaks into Psicone that night to investigate. A bit of scrounging in Vakuse's office reveals that schematics for the Games Generator have been stolen, and the group tracks the theft down to the Games Generator. In order to see if the Generator has been tampered with, the trio hooks themselves up and activates the machine, but a strange things happens.
Now in the game, Morgan, Dave, and George, now Zitz, Rash, and Pimple, respectively, find themselves surrounded by rats. The 'Toads then find the Dark Queen and Volkmire standing nearby. Volkmire reveals that he teamed with the Dark Queen and sabotaged the Games Generator out of jealousy for always being stuck behind the scenes while the 'Toads got all the attention. The Dark Queen, however, reveals a far more shocking truth: the so-called gameworld is actually a parallel universe, which the Games Generator created a portal to. She had ruled unopposed until the Battletoads were created at Psicone. And now, thanks to a virus she and Silas had injected into the Generator, the trio are now trapped in this universe and trapped as their own game characters.
Deciding to end the game at last, the Dark Queen sics her armies of rats on the 'Toads. Despite a valiant effort, attrition eventually begins to doom their chances. Fortunately, at the last second, they are airlifted out of danger and brought to a strange spacecraft.
Inside, the 'Toads meet Professor T-Bird, who admits to once having a relationship with the Dark Queen, but now needs help in stopping her evil plans. With T-Bird's aid, they're able to escape pursuit from the Dark Queen. Seeing as how they're trapped, the 'Toads decide to aid T-Bird as partners.
Part 2 is generally a recap of events from the NES game, with T-Bird and the Dark Queen commentating the action. After victories in Ragnarok's Canyon and the Wookie Hole, Rash and Zitz barely hang on for dear life in the infamous Turbo Tunnel. Later, they manage to slip out of the Arctic Caverns and into Surf City, where they blaze through easily despite Zitz having some trouble.
After the next scene in Karnath's Lair, Silas Volkmire provides his own sadistic humor in narrating the 'Toads taking a rather nasty fall in Volkmire's Inferno... one that Volkmire is continuously looping ad nauseum.
Back with the main action, the 'Toads continue through the Intruder Excluder and Terra Tubes, then survive the Rat Race. Finally, after the chaos of Clinger-Winger, Rash and Zitz climb the Dark Queen's Tower for the final battle...