Produced by TV Aichi, Weve, Tokyu Agency and animated by Gonzo, the series is directed by Hiroyuki Kakudō and Manabu Ono, with Hiro Masaki handling series composition, Takashi Kumazen designing the characters, Mitsuru Ōwa serving as the mechanical and prop designer and Megumi Ōhashi composing the music.

However, the Japanese production did not follow through on this intent, scripting the series as an independent story unconnected to the preceding shows.

[2] The English dub partially modified the series to establish links back to Armada and Energon, including changes to dialogue and small portions of new animation.

As this occurs, Optimus Prime's elite team of Autobot warriors are approached by the ancient Transformer Vector Prime, who has emerged from his resting place in the void outside of time to inform them of the legendary Cyber Planet Keys, ancient artifacts of power which can stop the black hole and save the universe.

Lost due to an accident during an attempt to create a cross-universal space bridge network, the Cyber Planet Keys now reside on four worlds somewhere in the universe – unfortunately, Vector Prime's map showing their location is stolen by the Decepticon leader Megatron, and both forces relocate to Earth as the race to find them begins.

On Earth, the Autobots befriend three human children named Coby, Bud and Lori who aid them in locating the Omega Lock, the focusing device for the Cyber Planet Key's power.

Megatron ingratiates himself with Jungle Planet's own dictator Scourge while his scheming lieutenant Starscream teams up with the mysterious Sideways, working towards his own goals.

With their forces bolstered by the ancient Autobots from Earth and the arrival of Wing Saber, who combines with Optimus Prime, the Autobots fight their way through a vengeful Megatron and defeat Starscream – but the battle is not without casualties, as Hot Shot, Red Alert and Scattershot are gravely wounded and rebuilt into the even more powerful "Cybertron Defense Team".

Gigantion, however, exists in another dimension, having fallen through a rift in space/time, and except for the kids and the Minicons, the others can't enter without having their minds separated from their bodies.

Luckily, Red Alert has created a vaccine program (based on Technology from Vector Prime's sword) to help but it is revealed that Jetfire has Trypanophobia and while the Autobots are able to reach the planet, the Decepticons are led there by the enigmatic Soundwave.

Galvatron blasts them and Starscream into another dimension and acquires the Lock and Keys for himself, intending to use their power to accelerate the universal degeneration caused by the black hole and remake the cosmos in his own image.

Vector Prime sacrifices his life to allow the Autobots to return to their home universe, and the five planet leaders confront Galvatron within the black hole and defeat him.

With all the Cyber Planet Keys now in his possession, Primus uses their power to finally seal the black hole, ending its threat.

With this final victory, Optimus Prime begins a new space bridge initiative, and the Transformers set sail for the four corners of the universe, and new adventures.

Finally, the Autobots found the Cyber Planet Keys and the Omega Lock, and awoke Primus, who shut down the black hole, saving Cybertron and the universe.

Although it has the same idea of searching for Chip Squares and Planet Forces to extinguish the Grand Black Hole as in the anime, the storyline development and characterizations are unique.

"Michael Drucker at IGN, reviewed the Transformers Cybertron: A New Beginning DVD, criticizing it as "A lackluster update on classic characters with minimal plot".