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Season 3
FF of Darkness 1
FF of Darkness 2
FF of Darkness 3
FF of Darkness 4
FF of Darkness 5
The Killing Jar
Dark Awakening
Forever is a Long Time Coming
Fight or Flee
Thief in the Night
Starscream's Ghost
Ghost in the Machine
Surprise Party
Madman's Paradise
Nightmare Planet
Carnage in C-Minor
Big Broadcast of 2006
The Quintesson Journal
Dweller in the Depths
Only Human
The Ultimate Weapon
The Face Of Ninjika
Call of the Primitives
Grimlock's New Brain
Money Is Everything
The Burden Hardest to Bear
The Return Of Optimus Prime 1
The Return Of Optimus Prime 2


The first portion of the story takes place simultaneously with the ending of "Dark Awakening". Gregory Swafford and Jessica Morgan, human scientists are near a remote star system to test a new heat resistant alloy on their ship, when they intercept the Autobot Flagship with Optimus Prime's body on board. The two humans dock with the ship and rescue Optimus' body, despite Gregory's hatred for Cybertronians. Their ship survives the star going nova, thanks to the alloy, but they also find a type of spore ejected from the star.

Months later, back on Earth, the Terrorcons attack Swafford and Morgan's lab to steal the heat resistant metal. They also discover that any being exposed to the solar spores goes mad with hatred and attacks every other being around it, spreading the Madness Plague by touch. The Protectobots and Technobots show up and fight the Terrorcons, but the Decepticon monsters escape with all of the alloy. Part of the lab is destroyed, and Jessica Morgan is injured. After the Protectobots race her to the hospital, Jessica's father, Dr. Morgan, declares his hatred for all Transformers for causing his daughter's harm. Gregory and Dr. Morgan hatch a plan to use Optimus Prime to destroy the Autobots. As surgeons operate on Jessica's body, Swafford and Dr. Morgan futily attempt to repair Optimus Prime's body. Jessica is released from the hospital paralyzed, but able to walk thanks to a thin Exoskeleton provided by the Autobots. Jessica stops her father from melting Optimus' body, so her Father convinces her to tell the Autobots that they have Optimus Prime's body.

Jessica informs Rodimus Prime and Ultra Magnus about Optimus Prime's location, but warns them that her father may deal treacherously with the Autobots. Ratbat spies upon them and reports what Jessica says to Galvatron. Rodimus and Jessica enter through the front of the lab, to distract the scientists, while the Aerialbots, Ultra Magnus and the Throttlebots sneak around the back to retrieve Optimus' body. As Rodimus & Jessica enter, they find Optimus Prime's body in the front of the lab, rather than the back. Then they see a trap sprung in the back of the lab. As the other Autobots walk into the back of the lab, the building seals them in and sprays them with the Hate Spores. The Autobots all begin to attack each other in the back of the lab, while Jessica and Rodimus flee with Optimus' body, trying to avoid infection. As they attempt to exit, they are blocked by Galvatron and the Decepticons, who seek to destroy Optimus Prime completely. The infected Autobots break out of the lab and infect all of the Decepticons present, except for Galvatron. Rodimus and Jessica escape from the building, as does Galvatron. Superion, infected by the Hate Plague, infects Defensor and severely damages Kup, Blurr, Wheelie, Bumblebee and Steeljaw.

Back in Autobot City, Wreck-Gar reports to Rodimus that he cannot revive Optimus Prime. Rodimus Prime surmises that the Quintessons may be able to revive Optimus, and sends SkyLynx to fetch a Quintesson. Rodimus races to shut Metroplex down before the giant Autobot can be infected. He shuts the city down, but is attacked by Ultra Magnus. Rodimus is rescued by Wreck-Gar, but Ultra Magnus infects the Junkion leader, who then infects Rodimus. The Hate Plague spreads across the Earth through the human population and the world plunges into chaos.

Elsewhere SkyLynx finds a Quintesson, on the run from some infected Sharkticons. The Quintesson agrees to help the Autobots if SkyLynx will save him from the infected robots. The Quintesson and SkyLynx work diligently on Earth and restore Optimus Prime to life.

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