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.
Adaptive Ability: The Aerospace Extermination Squadron drones can adapt to anything thrown at them, as Nightbeat and his crew learn first-hand. When they reappear in the on-going, they've lost this ability.
A Day in the Limelight: The War Within: The Age of Wrath gives focus to the Turbomasters, who came from the tail-end of the original toyline, and Flash in particular.
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.
All There in the Manual: The trade paperbacks of The Dark Ages contains some background information on each faction involved.
The More Than Meets The Eye profile series introduce a lot of characters who never got a chance to appear in the comics, along with establishing this continuity's versions of Megatron and Dinobot.
Anti-Hero: The Dinobots. As Grimlock put it, they don't like the Autobots, but they hate the Decepticons more.
Ascended Extra: Sunstorm, a background character from a single scene of the first TV episode, has an arc dedicated to him.
Badass Crew: The Wreckers turn up in the War Within, and the second mini-series.
The Dinobots, as well. They formed their own faction, the Lightning Strike Coalition.
Barehanded Blade Block: During the second War Within mini-series, the Fallen catches Grimlock's energo-sword in one hand.
Big Bad: Shockwave is responsible for pretty much every bad thing that happens.
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).
Combining Mecha: Devastator, Menasor, Bruticus and Predaking show up on the Decepticon side, while the Autobots have Superion and Defensor. Early on in the war, they're treated like superweapons, with each side hoping to have as many as possible.
Cool Spaceship: The Ark, same as usual. It gets blown up at the beginning of the ongoing, in an attempt to defeat Bruticus.
Curb-Stomp Battle: The Autobots versus Trypticon. They only survive because Grimlock called him elsewhere with a falsified distress signal.
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.
Deus ex Machina: A very literal one at the end of The Dark Age, when Primus appears to kill The Fallen.
Diabolus Ex Nihilo: The Fallen just appears at the beginning of the Dark Age. It's explained that Megatron's fooling around with Space Bridge tech is what freed him from "un-space".
Downer Ending: The ending of "Prime Directive" is really depressing. The Autobots drive off the Decepticons but San Francisco 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.
Enemy Mine: Shockwave and Jetfire, in The Dark Ages, agree to share information and figure out who's manipulating everyone behind the scenes. Then Grimlock interrupts.
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.
Fantastic Nuke: Combiners are treated like this in The Dark Ages, with a treaty signed banning them from aligning with anyone. Considering Springer's remark that Devestator and Defensor brawling could knock Cybertron out of orbit, there's a good reason for this.
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.
Funny Background Event: When Shockwave and Prowl are discussing a team-up in one issue of the War Within, Slag takes a moment to randomly punch Shrapnel to the ground.
Heroic Fatigue: Megatron tries to give Optimus Prime this in the first miniseries to make him turn his back on humanity.
A House Divided: Without Optimus to lead them, the Autobots split up into multiple factions. It's implied to be because Prowl was in charge.
Humongous Mecha: We get a brief glimpse of Fortress Maximus in the War Within, and he's the largest 'bot we see in the setting, towering over all his troops and the landscape around them.
Had he appeared in-fiction, Metroplex (whom the Autobots were creating in the on-going) would have been even bigger.
Irony: Snarl mocks Trypticon's dinosaur-esque design, years before he ends up with a dinosaur-based alt-mode himself.
The Juggernaut: The Fallen isn't stopped by anything thrown at him. It takes a very literal Deus ex Machina to stop him. Justified since he's one of the Thirteen, created to fight Unicron. Regular weaponry isn't going to do squat to him.
Mind Screw: The Fallen shows Bludgeon a vision of numerous skull-themed heads screaming at him. It's not explained what that all means, but it was probably meant to be the inspiration for Bludgeon's skull-faced Pretender shell.
Myth Arc: The series was trying to build up to one big arc involving the Quintessons 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.
Prequel: The War Within happens before the events of the main book.
Put on a Bus: Megatron and Optimus are absent for the second War Within mini-series. Megatron returns at the end of the first issue of the third series, but due to being cut short, Optimus never comes back. The unreleased issues reveal that they wound up on Quintessa, which means they effectively got Put on a Bus to Hell.
Quirky Miniboss Squad: The Fallen created one of these in the War Within comic series. Decepticon mystics Bludgeon, Bugly, and Mindwipe made a very effective one, too.
Start My Own: When Optimus and Megatron go missing in the Dark Ages, several Autobots and Decepticons split off and form their own factions.
Grimlock and the Dinobots form the Lightning Strike Coalition.
The Wreckers, led by Springer, take off on their own.
Every combining team has to go on their own.
Ratbat forms the Ultracons.
And Starscream forms a version of the Predacons.
Take That: The comics feature a lot of jabs against the mostly-forgotten competitor to the original, Challenge Of The Go Bots, 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.