The Decepticon attack on the Autobots comes to an abrupt halt when Galvatron and the Sweeps start firing at them. The Decepticons pledge with allegiance to Galvatron, but he wants to know who had been leading them. They point out the Quintesson ship nearby, so he decides to pay them a visit. Meanwhile, Rodimus and Ultra Magnus find a communications device, and use it to contact Wreck-Gar. Elsewhere, Earth Defense Command member Marissa Faireborn is sent to Io, to search for Blurr and Wheelie. She finds them, but her ship is attacked and destroyed by some lightpole creatures. With no way of getting back to Earth, they look into fixing the ship's radio.

Galvatron starts threatening the Quintessons, but they tell him about the Decepticons Matrix of Leadership. Galvatron says he's never heard of such a thing, but the Quintessons want him to destroy the Autobots on Goo in return for this information. However, the Junkions then arrive and help the Autobots, freeing them from the Goo and getting them into their ship. Judge Deliberata manages to escape, and heads back to the Quintesson ship after being punched out the way by Galvatron. Galvatron attempts to stop the Junkions, but they're able to escape, leading to him declaring that the Junkions will share the same fate as the Autobots. He returns to the Quintesson ship, where an alliance between the Decepticons and Quintessons is formed. They intend to attack Earth and Cybertron at the same time, with the Quintessons wanting to wipe out the humans as well as the Autobots -the human's association with the Autobots has changed the latter.

The Junkions return to the Planet of Junk, where Springer is put back together and revived. Rodimus says he's been thinking about the Quintessons, so Springer jokingly suggests Rodimus gets blasted again so he can enter the Matrix. As he and Arcee walk off, Rodimus deactivates himself, allowing him to enter the Matrix and meet with the spirits of previous Autobot leaders. They tell him about Cybertron's past, and how the planet was originally a factory created by the Quintessons. The Quintessons built two types of robot: military hardware and consumer goods, the lineral ancestors of Decepticons and Autobots.

However these robots evolved and turned on the Quintessons, eventually leading to the Quintessons getting forced off Cybertron. A period of peace followed, but soon the Decepticons began their plans for conquest. The Autobots developed the art of transforming, something the Decepticons copied and the wars go on to this day. Optimus Prime tells Rodimus the Quintessons have been waiting to strike so they can reclaim Cybertron from the Transformers. Rodimus wakes up and tells the other Autobots they must return to Cybertron now, as the planet is in great danger.

On Earth, the Constructicons finish their work on Trypticon, a city-sized Transformer who is to destroy Autobot City. The Quintessons then use a decoy ship to destroy Cybertron's main power station, allowing the Decepticons and Quintessons to begin their attack on the planet. As the Decepticons start firing, the Quintessons watch and say that soon, Cybertron will be theirs!

Notes

-Eric Idle voiced Wreck-Gar in the Transformers movie, but for his appearances in the third season, he's voiced by Tony Pope.

-The lightpoles aren't named in the episode itself, but are in the script. They seem to have changed a bit since they were last seen at the end of the previous part, as there they were more like giant monsters, whilst here they are smaller, bat-like creatures.

-The Japanese dub of the episode changed some of the dialogue for Trypticon's creation, as in the Japanese continuity, Trypticon had already been built. Instead, the Constructicons are reactivating Trypticon, rather than constructing him.

Errors

-The Decepticon's lasers are colored yellow instead of pink during this shot.
-The Autobots just casually walk right towards the Decepticons, who are firing everything they've got at them... although the Decepticons are also somehow missing with every shot.
-Slag is present during this shot, who isn't meant to be there.
-Dead End and Blast Off's conversation seems to abruptly get cut off before it can be finished.
-When the first group of Decepticons are shown getting blasted, the lasers are colored yellow instead of pink.
-During this shot, most of the Decepticons are firing yellow lasers instead of pink (Galvatron's lasers are colored correctly though!).
-Motormaster's "Galvatron, you have returned!" line is not spoken by his normal voice actor, Roger C. Carmel. His other lines are voiced by the correct voice actor.
-Skydive, an Aerialbot, is with Swindle and Motormaster when they hail Galvatron.
-During this shot you can see two unidentified Autobots stood behind Kup, colored gray and green.
-The Constructicons are shown creating Megatron, which doesn't really work given that Megatron stated they built the Constructicons on Earth in season one, which was later retconned to say Megatron turned the Constructicons to evil in season two.
-There are also eight Constructicons present rather than the usual six.
-The Autobot who passes Alpha Trion the Matrix has his arm colored like Optimus Prime's during this shot. The Matrix is also much larger than usual.
-Vortex is colored like Octane during this shot.
-Long Haul is colored completely wrong during this shot. Oddly, after tightening a nut on the thing he's working on, he then proceeds to tear it off entirely!
-Long Haul is colored wrong again during this shot.
-When the Constructicons start celebrating, they are colored like they're several different Autobots: Ultra Magnus, Kup, Perceptor, Wheelie and Arcee.
-Perceptor is colored like Grimlock during this shot.
-The Aerialbots all have the wrong colors during this shot. They appear to be colored like Marissa's ship seen earlier in the episode.