In 2002, a new Transformers Generation 1 comic was published by Dreamwave Productions, alongside an adaptation of the Unicron Trilogy (Armada, Energon, and Cybertron); this was the first to officially use the title Generation One. Simon Furman was brought back to write parts of it, as well as several lesser-known writers. It began as a set of mini-series which gave rise to a short-lived ongoing title. Ideas were taken from both the G1 cartoon and the Marvel comic, and even Beast Wars.The main draw of the Dreamwave comic was the highly detailed, manga-influenced artwork of Pat Lee - which, as it turned out, included a lot of Dull Surprise and vaguely sexual poses. However, most of the actual drawing, colouring, and inking was done by uncredited and frequently unpaid guest artists while Lee was buying fast cars and sponsoring his girlfriend's Miss World campaign. Following a series of unethical business practises, scandals, and outright crime, Dreamwave declared bankruptcy, leaving both the G1 and Unicron Trilogy stories unfinished.
Generation One-related series published by Dreamwave:
Prime Directive (April-December, 2002). 6 issues.
The War Within (October, 2002-March, 2003). 6 issues.
War and Peace (April-October, 2003). 6 issues.
The War Within: The Dark Ages (October, 2003-April, 2004).
Generation One (December, 2003-December, 2004). 11 issues, though numbering started with issue #0.
Micromasters (July-November, 2004). 4 issues.
The War Within: The Age of Wrath (September-December, 2004). 3 issues.
Aliens Are Bastards: Much of America's population comes to this conclusion concerning the Transformers after they are forced to destroy an oil refinery against their will (which no one else knew) and the Decepticons attacked San Francisco.
Ascended Extra: Sunstorm, a background character from a single scene of the first TV episode, has an arc dedicated to him.
Barehanded Blade Block: During the second War Within mini-series, the Fallen catches Grimlock's energo-sword in one hand.
Broad Strokes: This continuity takes place in a variation of the G1 cartoon continuity where the first two seasons of the cartoon occurred but were different from the original show (for example, the Combaticons being built on an island is brought up but they're from Cybertron instead of being built on Earth).
Cut Short: Perhaps one of the worst examples. Being cut short resulted in nearly every storyline in the comics being cut off. At the time it ended the series had set up dozens of storylines both major and minor.
Darker and Edgier: Than the G1 cartoon. The first mini-series in particular is much darker and has a bleak and depressing tone. Thankfully the writers afterwards lightened things up.
Downer Ending: The ending of "Prime Directive" is really depressing. The Autobots drive off the Decepticons but the city is in ruins, hundreds are dead including the Aerielbots and Constructicons, Wheeljack is practically in a coma, most of humanity hates or distrusts the Autobots now, Grimlock refuses an offer from Optimus Prime to become good again, and Prime's idealism is near it's breaking point. It ends with Prime noting that chances are, it's still gonna get worse from here.
Early-Installment Weirdness: The first miniseries treats the comic as if it's set in the Generation One cartoon continuity (or rather, a variant of it). Later issues would establish that this series is it's own timeline.
Evil Plan: Shockwave starts doing some serious ones and as the series goes on it turns out that Shockwave was responsible for pretty much everything that's happening. It takes Optimus Prime, Ultra Magnus, Starscream, and all of the Autobots to finally derail it.
Face-Heel Turn: Grimlock pulls one in the first miniseries and joins up with the Decepticons. But then the second miniseries reveals that Megatron forced him into it by kidnapping the other Dinobots.
In issue 8 of the ongoing it's strongly implied that Bumper has pulled one and is now an agent for the Decepticons, but due to being Cut Short we'll never find out if this was true.
Flat Earth Atheist: Jetfire, though it's not nearly as unjustified in this continuity. In fact, all things considered, it was quite understandable until the Fallen showed up.
Heroic Fatigue: Megatron tries to give Optimus Prime this in the first miniseries to make him turn his back on humanity.
Myth Arc: The series was trying to build up to one big arc involving the Quintessens and Megatron. Due to being cut short we never saw the resolution to the arc. Apparently Unicron, the female Transformers, the Golden Disk, the Micromasters, The Great Shutdown, and Earth itself are all somehow linked to this conspiracy.
Take That: The comics feature a lot of jabs against the mostly-forgotten competitor to the original, Challenge of the GoBots, mostly in the form of background characters resembling the Go Bots being killed in various ways.
The Starscream: The trope namer is a main character so what do you expect?
Word of Gay - Sunstreaker was outed by Matt Moylan, no matter how illogical this may have been for a genderless robot. The comics were getting ready to explain how the whole gender and reproduction thing worked for Transformers but due to being cut short the plotline went unresolved.