Goofs: When Optimus orders the Autobots to transform and roll out, all do so, moving forward, except Kup, who faces the other way and moves in reverse.
When Galvatron is threatening Optimus, his cannon has a trigger on it.
In the final scene after Optimus shakes hands with Galvatron, he says 'Autobots transform and roll out', in the scene after that we see in vehicle modes Optimus (who is not white), Kup, Goldbug and Blurr driving off into the sunset away from a deactivate Metroplex. But the scene before that had Hot Rod and Magnus present, while Goldbug and Blurr weren't present. This final scene was most likely meant to be near the beginning of the episode when Optimus tells the Autobots to transform and roll out as they're getting ready to go to Charr to get the metal, since Blurr and Goldbug were present back then, this is most likely a production order error.
Although Blaster appears in this episode, he doesn't speak even once. Very unusual considering the talkative nature of this character.
After the decision is made to go to Charr and take back the metal and Optimus gives the order "Autobots, transform and roll out," Kup transforms and then drives off backwards.
When Jessica reacts to seeing the spider, she isn't wearing her exo suit.
Supposedly Kup, Steeljaw, Bumblee and Wheelie were the only Autobots besides Skylynx himself to escape being infected, but we see Blaster in Optimus's party a few times.
Goldbug and Blaster were infected with the hate plague even though nobody touched them.
At the beginning of the episode, Optimus is seen removing wires/tubes from himself. In the last episode, he didn't have any wires or tubes attached to him when he was revived.
In Aerial Assault, a device installed in all combat Transformers called a weapons console is discussed. It can make their guns appear from nowhere and controls their inbuilt weapons (as demonstrated by Slingshot, who needed to replace his missing console).
So, therefore, combat Transfomers do not need to be given their own guns.
Sky Lynx gives Optimus a summary of what happened after Optimus is revived. However, most of the events Sky Lynx describes occured while he was searching for the Quintesson, and Rodimus never briefed Sky Lynx when he was assigned his mission.
How did Kup know that Rodimus had been contaminated since he was deactivated by Superion before Rodimus was.
While Rodimus is struggling with Optimus in the factory Rodimus's aura disappears when he kicks Optimus off him.
When Rodimus is standing behind some scrap metal out in the Scrap yard his Aura is shining through it.
The Autobots Sky Lynx lists as not being contaminated by the hate plaque are Kup/Wheelie/Blur/Steal Jaw and Bumblebee. Yet when they are repaired by the Quintesson, Wheelie is not among them but Blaster who was not mentioned is.
When Optimus and Sky Lynx are escaping from Char with the metal Optimus is already grey.
Optimus Prime is supposed to be back to his regular colors during the last scene, but he is seen going back and forth between being all white and colored.
Jessica's aura is gone when she grabs onto Sky Lynx's tail.
Goofs: When Optimus and SkyLynx escape after Jessica and Galvatron become infected,Sky Lynx doesn't become infected when Jessica grabbed onto his tail and Optimus looks as if he was coated with the special metal before undergoing the process.
After Optimus removes the Matrix from Rodimus, Rodimus doesn't revert back to Hot Rod.
Autobot Elder: The plague you speak of has visited us once before. A wise man was able to contain the spores and send them into the sun, but no one was able to destroy them, no one had the power to do that. The only way to fight such madness is with wisdom! Unfortunately, not one person now has the wisdom to contain the spores... much less destroy them now that they spread across the galaxy.
Optimus Prime: Perhaps there does exist a source of wisdom powerful enough to destroy the spores and cure the entire world... The accumulated wisdom that resides within the maxtrix.
Rodimus: (sing-songy) Come out, come out where ever you are. (shouts) I know you're in here! Can Optimus come out and play?
Galvatron: Come on, Optimus, tell me. What's so special about the metal? How will it be used? Why's it so important?
Optimus: I've already explained it to you.
Galvatron: You told me it was important, but you didn't tell me why.
Optimus: That's because I know you all too well, Galvatron.
Cyclonus: Join us, Galvatron.
Galvatron: Die, you worthless piece of slag!
Quintesson: No, please! Stop!
Galvatron: Never, Quintesson! This world is ours now! Optimus Prime shall die again! ( Lights start coming out of Optimus. Galvatron backs up)
What is this?
Optimus Prime:( Rising and opening the matrix) Now light our darkest hour.
Optimus Prime: No more games, Rodimus! Innocent lives are at stake!
Rodimus Prime: No one is innocent!
Galvatron: There will be no war today, Optimus Prime. You have earned Galvatron's respect.
Hot Rod: The wisdom of the ages? It's lost.
Optimus Prime: No, not lost. We're all a little wiser now.
Hot Rod: But the matrix is empty?
Optimus Prime: It's up to all of us to fill it again. With the wisdom we accumulate from this moment on. Autobots! Transform, and roll out!
Last appearance of the Sweeps.
Galvatron seems extremely rational in this episode, which is very different from the maniacal behavior he usually exhibited all season. Perhaps being around Optimus brought out more of the rational Megatron part of his personality.
Galvatron's rationality may be due to having received some of the wisdom and knowledge from the Matrix, remember Prime said the wisdom is not lost, "we're all a little wiser now"
Last appearances of Breakdown, Dead End, Motormaster, and Wildrider.
Last appearances of the Predacons and their combined form of Predaking.
Although not directly stated, Optimus seems to know that Galavatron was once Megatron with the statement, "I know you all too well, Galvatron."
Last appearances of Blaster, Sky Lynx, and Steeljaw.
When Optimus delves into the Matrix, the Autobot leader who tells him the history of the hate plague looks remarkably like one of the faces of the Quintesson.
First appearance of Goldbug (the new form of Bumblebee).
Last episode to be animated by the japanese studio, Toei.
"The Touch" by Stan Bush can be heard in this episode when Optimus Prime opens the Matrix. The song was the main theme in the Transformers movie.
Optimus Prime: Now light our darkest hour!
This is probably from The Trasnformers: The Movie, where Rodimus Prime said the exact same line before the destruction of Unicron.