- A new human organization, known as the Protectorate, is formed as direct competition to the EDC and United Nations. They are backed by numerous former UN nations, including most of Asia. The Protectorate advocate a pro-human, anti-robot policy.
- An annoying alien named Jigsaw repeatedly throws Autobots and Decepticons into various traps. He is eventually discovered and defeated, though his motives remain a mystery.
- A nest of 'space dragons' is discovered on the Moon. After various skirmishes, the Decepticons lure them into attacking Alameda, where they are nearly wiped out.
- Decepticonz makes its debut. Primus rolls over in his grave.
- A long lost Autobot lava prison planet, designated P-19170167 and created eons ago by Elita One, is thrown into chaos by a massive riot by the prisoners. Forced to break radio silence, Autobots and Decepticons rush to aid their respective comrades. Among others, Dreadwind, Darkwing, Snapdragon, Impactor, Nightbeat, and Quickswitch are rescued. The prison is destroyed by the merged form of Dreadwing, and the planet is abandoned.
- The Muffin Man strikes.
- In an alternate future, a mysterious mech named Praxis experiments with time travel.
- Cybertron is no more, Earth is devastated, and the Autobots and Decepticons are shattered. The crazed Cybertronian scientist Praxis rules over what is left with an iron fist, and seeks to cement his power with time travel experiments.
- Praxis is revealed to be a twisted version of Skids. He and his scientist allies are eventually overthrown. Praxis is slain.
- Main article: Space Dragons
Autobot and Decepticon forces discovered organic alien creatures, dubbed space dragons, hidden in craters in the moon caused by a 'meteor shower'. After numerous run-ins, Geist coerced the dragons to attack Alameda, where the dragons and its queen were sadly annihilated.
- Main article: Prison Planet
A forgotten Autobot prison camp located on a backwater hellhole of a planet was rediscovered when the Decepticon inmates got loose and threatened to kill their Autobot guards, prompting both sides to rescue their various factionmates. This TP served to introduce Impactor, Quickswitch, Nightbeat, Snapdragon, Dreadwind, and Darkwing.
- Droning On - The Junkion Leet decides that he needs a new pet. Unfortunately the object of his affection is Shockwave's personal drone. A terrible disaster ensues!
- Bidding on DOOM - Leet is outbid on an anti-gravity disk on ebay. The only solution - find and steal it!
Soundwave's Human Sensitivity Training Sessions
- Main article: Soundwave's Human Sensitivity Training Sessions
- Human Sensitivity Training - Soundwave enlists Tuxedo to help train the Decepticons on how to treat humans as if the Decepticons really, truly respect them.
- Human Sensitivity Training pt 2 - Soundwave tries desperately to train several of the most idiotic Decepticons on how best to treat their human "allies," and the results are catastrophic.
- Main article: Decepticonz
Soundwave began transmitting the ever-popular Decepticonz, which is still ongoing in some incarnation to this very day.
- Main article: WW2 Altmodes
A mysterious 'transmorgification' energy wave alters the design of many Transformers - when they transform, they become WW2-era counterparts of their normal alternate forms.
- Of Sweet Birds and Fly Cats - Retro WWII Mayhem!
- TNF 11/14/07 - Anti-gestalt training - During Autobot training week, Durango hosts a training session concentrating on urban combat and anti-combiner tactics.
- Escape From Cygnus Beta - Three Autobots, Paradigm, Mishap and Gantry escape from a Decepticon prison and await pickup. Nothing can go wrong now, surely?
- Autobots raid Magnaron! - The title says it all.
- Chinese Cheating - With the Decepticons unable to raid most of the world due to a deal with the Protectorate, Blueshift and Fulcrum develop a cunning plan!
Airbase Argosy Prelude
- Main article: Airbase Argosy
Before the Decepticon Airbase Argosy could be completed, Fusillade and the Decepticons had to acquire the resources and raw materials for the massive construction project.
- Hephaestus: The Hijacking - The Decepticons hijack the UNS Supertanker Hephaestus, full of crude oil and raw materials.
- Hephaestus: Hostage Rescue - The Autobots respond, launching an operation to free the human crew now being held as hostages. Featuring a battle of the tapes: Ravage vs Frostbite
- Log: Epic Paris G-Battle - Three Decepticon and two Autobot combiners, plus assorted Autobots, go at it in Paris as what should be a simple raid balloons into an out-of-control clash of the titans!
Here Comes Tomorrow (Alternate 2107)
- Main article: Here Comes Tomorrow
It is the year 2107, a dark future. Cybertron is no more, Earth is devastated, and the Autobots and Decepticons are shattered. The crazed Cybertronian scientist Praxis rules over what is left with an iron fist, and seeks to cement his power with his time travel experiments...
- Lies, Damn Lies, And Statistics - Sixknight and Grimlock vie with each other to get the dreaded Church of Primus on side.
- Brothers In Armour - Sixknight vs Moonracer. Greatshot vs Astrotrain. One of them will die today.
- ...All This And Civil War 2 - Sixknight deals with a very unhappy Fusillade
- Living The Dream - Sixknight kills Daniel, again and again and again. And then... I, WARMONGER!
- All You Ever Wanted To Know About Six (But Were Afraid To Ask) - The worm has turned. As the endgame nears, Sixknight fights his brother Greatshot in a battle to the death!
- Lair Of The Beast - Praxis summons his minions to him to prepare for the final conflict
- Final Crisis - The forces of Praxis fight the forces of Grimlock in an epic battle to determine the fate of the planet, past and future
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