The Search for Alpha Trion

Optimus Prime races to rescue the female Autobots' leader Elita-One and uncover the secret of his own creation.

On Cybertron, three Female Autobots (Chromia, Moonracer and Firestar) sneak into Shockwave's headquarters under orders of their leader, Elita One. They raid Shockwave's stockpile of energon cubes to power their fight against the Decepticons. On the way out, Moonracer decides to try and take some extra Energon, as they desperately need it, and accidentally trips an alarm and is trapped. Firestar is sent ahead while Chromia tries to shoot Moonracer free, but the cage doesn't budge. Shockwave, surprised to see female Autobots still alive, accidentally frees Moonracer and fails to stop them from escaping when he is stunned by being hit with some energon cubes. He does send a sentinel after them, but it's shot down by Moonracer.

The Female Autobots escape the sentinel and return to Elita One, though Shockwave deduces the approximate location of their underground headquarters. Shockwave contacts Megatron who sends Starscream, Astrotrain, Rumble and Ramjet to assist in the apprehension of the Female Autobots. Rumble starts an earthquake which damages their headquarters. Elita One attempts to lure them away from the base by attacking, but is captured. Rumble continues shaking things up until Starscream believes the base is suitably destroyed, though the Female Autobots have actually survived.

Megatron contacts Optimus Prime and shows him the imprisoned Elita One. Optimus rushes to her rescue, even though he knows it's a trap. Apparently, 4 million years ago, Optimus and Elita had a "thing" going. Right before boarding the Ark, Elita begged to go with him, but Optimus told her it was too dangerous. As they spoke, the Decepticons attacked Iacon and Elita vanished in the chaos, leaving Optimus to think she had perished. Not wishing to lose her a second time, Optimus heads for Cybertron via the Decepticon space bridge. Powerglide, Ironhide and Inferno become curious as to why Optimus is heading to Cybertron alone and follow in secret.

As soon as Optimus arrives, he is taken prisoner by Starscream, who dangles him over a barrel of acid to torture Elita. Rumble drops Optimus, but before he lands in the barrel, Elita uses her special power, which stops time. Elita rescues Prime, but at the cost of her own life force, as the special power uses up so much energy. Prime loads Elita into his trailer and races to find Alpha Trion, the only Autobot who can save her.

Back at Shockwave's headquarters, the Decepticons believe Optimus had perished in the acid. Just then, the three Autobots arrive and attack. In the Female Autobots' underground headquarters, Moonracer comes up with a plan to dig their way out. They detonate the energon cubes they had stolen, creating an exit. They soon meet up with their male counterparts and together they take on the Decepticons.

Optimus eventually finds Alpha Trion's base‎, and the old Autobot uses his skill to repair Elita One as best he can. In the end, Alpha Trion instructs Prime to interface with her for a power transfusion, as he is the only Autobot compatible with her design. A confused Prime remarks that only his creator could know that. After the transfusion, Elita One recovers, and the two then return to help the Autobots fight off the Decepticons. Outnumbered, the Decepticons retreat. Alpha Trion then sets the Female Autobots up with a new secret base, and the two Autobot groups bid each other farewell when the Autobots prepare to return to Earth.

—Shockwave obviously hasn't kept up to date on Cybertron's Discovery Channel.

—Shockwave disses Chromia and gives Megatron material to rip off.

—Elita One need not worry about Man-Thing, then.

—Megatron calls to say he's discovered girls.

—Elita One's plea to Starscream to free Optimus Prime doesn't have the expected result.