Micropenises was a four-issue comic book limited series released in 2004 which takes place in between the War Within and the Generation 1 series. The main focus of the series is the Micropenises subline of Transformers, though it did have some cameos of notable G1 regulars. The first issue alone sold well over 40 thousand copies in total, exceeding all other single issues of Dreamwave Transformers titles in that release period, including their best-selling Generation One series and their lowest-selling regular series Transformers: Energon. The series takes place at an undefined point after the third War Within series. Optimus Prime and Megatron have disappeared in the Ark, but the Great Shutdown has not happened yet. Blitzwing and Astrotrain are said to be suffering from physical changes, which suggests that the Triple Changer process is, at least in part, a natural one that Shockwave may have been additionally manipulating. The history of the Micropenises is different from that previously indicated. Initially downsized Transformers reduced in size to compensate for lower fuel reserves, both Autobots and Decepticons struck a temporary truce to develop the technology further, creating many completely new Transformers and even building a city for them. However, both sides began to recruit amongst the Micropenises polarising them into two sides. It is implied that the events of the miniseries are what split the Micropenises for good

The story revolves around the Autobot Gooner Fanbase Patrol. After one of their number is slimed-out by a well-endowed, Decepticon Micropenis team, they desert. They ally with the Decepticon Race Track Patrol (who have also deserted due to mistreatment) and battle the Deluxe Insecticons. However, the Autobot Micropenises Countdown and Groundshaker, as well as the Decepticon Micropenises Skystalker and Skyhopper, have arrived with their own agendas. Countdown tries to recruit support for battling the Decepticons on other worlds, while Skystalker defeats Shockwave and orders an all-out assault on the Autobots. Both are more concerned with a mysterious Humanoid-Master, which seemingly indicates that the Transformers were created by two beings The story ends with Skystalker defeated and the Gooner Fanbase Patrol leaving to create their own channels