Issue #1 cover by Don Figueroa
The series debuted in July, 2006 and is set during the same time frame as The Transformers: Infiltration (the first issue shows Optimus Prime receiving Ironhide's call from Infiltration). It technically consists of issues seven through ten of the ongoing Transformers saga, which is split into arcs instead of being one complete series. The four-issue series was written by Simon Furman with art by Don Figueroa. Unlike Infiltration, the series is set almost entirely on Cybertron.
It is revealed gradually through flashbacks that during the war, the Decepticon scientist Thunderwing realized that the planet Cybertron was dying due to the adverse effects of the Autobot-Decepticon war. Trying and failing to convince his fellow scientists of the danger, he invented a process where a bio-mechanical symbiotic shell could be grafted to a Transformer. When this was rejected by Megatron, Thunderwing tested the process on himself. It worked, rendering him immensely powerful, but at a cost: it drove him mad, leading him to devastate large portions of Cybertron. A last-ditch alliance between Optimus Prime and Megatron stopped the creature when it fell into the depths of Cybertron, but Prime refused to allow Megatron to destroy their world to make sure of Thunderwing's destruction.
In the present, a scientific expedition consisting of Jetfire and the Technobots detects unusual energy readings on Cybertron. Investigating, they are captured by Bludgeon's cultists, and their ship is shot down, although not before the other Technobots release a message buoy. Bludgeon plans to reanimate Thunderwing using Ultra Energon, and send him out to destroy other worlds so that Cybertron may be reborn, unleashing him first on Nebulos. He also plans to give himself and the other cultists their own bio-mechanical shells. However, Prime has received the message buoy, and calls in the Wreckers to investigate.
On Nebulos, the local Decepticon infiltration cell led by Darkwing do their best against Thunderwing, but most of the group are summarily crushed. The Wreckers and Prime arrive on Cybertron, eliminating Bludgeon's cult. Bludgeon has tried the grafting process on himself, but has done it too soon: as with Thunderwing before him, it drives him mad. They destroy Thunderwing's control device, which causes him to return to Cybertron. Razorclaw informs Megatron (now on Earth) on Thunderwing's reemergence and Megatron orders him to do what is necessary to destroy the monster, even up to destroying Cybertron.
Thunderwing arrives, and the Wreckers, even with some unlikely assistance from Razorclaw's Decepticons, prove unable to halt it. However, Jetfire discerns a weakness: the more Thunderwing exerts himself, the faster the Ultra Energon powering him will burn out. Prime leads a host of Centurion robots into battle as Razorclaw prepares to obliterate Cybertron. Prime's last-ditch assault causes the beast to finally stop, simply shutting down, as the Decepticons abort the countdown with a second left to go. Prime then departs on the Ark-27, as Jetfire reports that Bludgeon got the Ultra Energon from Earth. Recalling a communication from Prowl's Earth unit before Thunderwing's rampage, Prime sets course for the now suddenly important planet, leading into the last page of Infiltration.
Relationship to other Transformers series
- Writer Simon Furman and artist Don Figueroa had previously collaborated on several Transformers projects for Dreamwave Productions, the now-bankrupt company that formerly was granted the Transformers license from Hasbro. They also reunited for IDW's two Beast Wars miniseries.
- Optimus Prime is seen in a pre-Earth form, which appears similar to his pre-Earth form in Dreamwave's The War Within series. Furman has said such a similarity is only coincidental.  Stormbringer artist Don Figueroa was also the penciller on The War Within volume 1.
- The Centurion drones of the story are a homage to the mechanoid of the same name that appeared in several of Simon Furman's Marvel UK Transformers strips.
- A sequel of sorts would occur in the Spotlight issue on Galvatron, which revealed what happened to Thunderwing's body after it shut down. The issue on Arcee would reveal Bludgeon's fate as well, revealing his Spark was incarcerated on Garrus-9.
- The conversation between Razorclaw and Megatron in Stormbringer #3 also takes place at the end of Infiltration #4, although the reader does not hear the full conversation until Stormbringer.
- It's unknown whether the Decepticons on Nebulos are binary-bonded yet. However, since they are acting in "Siege Mode" (i.e. covertly) it is unlikely. The Headmaster process was created on Earth in The Transformers: Devastation by Scorponok, so it is highly unlikely that any Transformers other than Scorponok and Sunstreaker are true Headmasters yet.
- The miniseries was promoted with the tagline "Nothing but robots on Cybertron!", referring to many fans' discontent over the human cast of Infiltration. The tagline wasn't entirely true — events also occurred on the planet Nebulos, a world populated by aliens of semi-humanoid appearance who feature in the Headmasters, Targetmasters and Powermasters Transformers toy line. Their appearance was minimal, though.
- Jetfire's design for Stormbringer was based upon his toy in the Transformers Classics toy line in 2006.
- Thunderwing in phase 2 battle form can be seen here  fighting both Autobots and Decepticons.
- All the Decepticon cultists seen here are Pretenders in the toy line. While they have not received their shells, the Decepticons are drawn so that their robot forms somewhat resemble their Pretender shells. Bludgeon's shell is seen, however — it bears a strong resemblance to his classic look, but has visible tank treads and turrets, suggesting it can transform into a tank.
- In Prime's flashback to Megatron rousing him in issue #1, it appears that the Matrix is semi-visible under Prime's cracked chest plate.
The trade paperback (TPB), originally slated for release in November 2006, was eventually released in February 2007, while a pocket sized "Manga" volume was released in April 2007. The TPB includes all the wraparound covers used throughout the series and some additional art by artist Don Figueroa. Included are robot and alternate modes for Optimus Prime, Megatron and Bludgeon, all of which were only seen in robot mode in the series. Concept art (in both modes) was included for Iguanus and Bomb-Burst. In addition, art was included for several characters not featured in the series such as Cosmos (robot mode), one of the Seekers (with 2 different robot and alternate modes) and Astrotrain (3 modes).