The Aerialbots fight some Decepticons and then return to base. Most of the Aerialbots were impressed with the Decepticon's battle skills, but their words annoy Ratchet and Ironhide. Optimus says the Aerialbots were only built a few weeks ago, they haven't been fighting the Decepticons for as long as they have. Teletraan I then reports strange energy readings coming from Cybertron itself, so the Autobots head there via Omega Supreme. At the Decepticon base, Megatron is angered that the Aerialbots threaten his supremacy of the skies. Soundwave reports that the Autobots have left for Cybertron, so the Decepticons use the space bridge to get their first. Megatron explains that Shockwave has been working on the kronosphere, a time machine he'd intended to use to go back in time and steal energy from Cybertron before the war had started. But now he intends to use it to get rid of the Aerialbots.

The Autobots arrive on Cybertron, but are attacked by Starscream, Thundercracker and Skywarp. The Aerialbots engage them, but then most of them stop, as Slingshot says they just want to talk. Starscream asks what they want to know, so Slingshot wants to know why Optimus Prime thinks they're evil. Starscream tells them to stick with him, as he'll teach them more about the Decepticons.

Starscream leads the Aerialbots to the kronosphere. Silverbolt runs over and warns his team not to go there, but as he gets to them, Megatron activates the kronosphere, sending the Aerialbots back in time. Megatron intends to send them back to the beginning of time, but the rest of the Autobots then arrive. Optimus shoots the kronosphere, damaging it, whilst the rest of the Decepticons retreat. The Autobots start to repair the kronosphere, as they realize that the Aerialbots have been sent back nine million years, to a time when Cybertron was in its golden age, and before the war started. The Aerialbots start looking around Cybertron. They meet Orion Pax, a worker who has a hangar full of energy. They also meet Orion's girlfriend, Aerial, along with his best friend, Dion. The group discuss these flying robots they've heard about, who in reality are the Decepticons. The Decepticons are building up an army, but the group believe the guardian robots will protect them.

The Aerialbots leave, but a little later on, Megatron appears and goes to the hangar. He meets Orion and asks if he could store his wares here. Orion shows him around the hangar, and explains they store energy here. As soon as Megatron hears this he orders his forces to attack. Orion tries to stop Megatron, but gets shot. Aerial then tries to protect Orion, but Megatron blasts her as well. Orion attempts to attack Megatron again, but Megatron shoots him again. The Decepticons storm the hangar, which results in Dion getting shot. The Aerialbots get back to the hangar, but they see the devastating results of the Decepticon's attack. They pick Orion up and take him to the next city, where they meet Alpha Trion. Alpha Trion has been building an army to combat the Decepticons, but he detects a strong spirit within Orion. He decides to totally rebuild him.

Sometime later, Alpha Trion finishes his work on Orion, changing him completely into a new Transformer: Optimus Prime! Optimus asks if Aerial could be rebuilt the same way he was. Alpha Trion says it could be done, and as Optimus and the Aerialbots leave, Alpha Trion muses over creating a female warrior... he decides to call her Elita One. Meanwhile, Optimus confronts Megatron, and starts gunning down his troops. Nearby, the Aerialbots find out that Megatron's drones are entering the hangar. Wanting to stop them from taking the energy, they enter the hangar and set explosives. But they then realize that the exits are blocked by the drones. They decide to blow up the hangar and sacrifice themselves, but as Slingshot sets the charges off, the repaired kronosphere is activated, and they are sent forwards in time.

They arrive back at the present day, where they help the Autobots destroy a guardian the Decepticons had reactivated, and also make the Decepticons retreat. Slingshot yells to Megatron, telling him that they'll never stop fighting until he's finished. Wheeljack asks what happened to them in the past, and Silverbolt says not much. They learned a few things about Megatron, and Optimus Prime... or should he say Orion Pax? Prime then realizes something -it was the Aerialbots who saved him! Ratchet asks what this is all about, but Silverbolt tells him to ask Prime -he knows. Prime says it all began about nine million years ago... to which Ratchet moans that it's going to be one of those long stories...

Notes

-It was mentioned in The Search for Alpha Trion that Alpha Trion was Optimus Prime's creator, and this was mentioned again in the second part of The Key to Vector Sigma. This episode actually shows how Optimus Prime came to be.

-Alpha Trion is never named in the episode. He has a slightly different design when compared to his previous appearances.

-Thundercracker and Alpha Trion were usually voiced by John Stephenson, but for this episode, Alpha Trion was voiced by Corey Burton, whilst Thundercracker's single line was provided by voice director Wally Burr.

-This is one of the most violent episodes of the series, with:
--Orion getting shot twice, the second blast going right through him.
--Aerial being blasted, with a load of smoke coming out of her.
--Dion and some other generic robot being gunned down.
--A guardian robot being shot in the head, which causes its head to explode (this is the one I'm amazed was allowed to air).
--Prime gunning down several of Megatron's troops, with each one exploding when hit.
--Superion hitting the guardian robot with enough force it breaks apart into pieces when it lands.

-Despite the above, writer David Wise has said in an interview it was originally even more violent -when Megatron shoots Orion for the first time, what was supposed to happen was his blast would have severed Orion's arm. Megatron would have then picked the arm up and used it to decapitate Orion! This bit was changed so Megatron shoots Orion through his chest.

-Another difference was that Aerial was originally supposed to die. But this was changed so Aerial would be reconstructed into Elita One.

-Fans have speculated what happened to Dion, with some believing he was rebuilt into Ironhide. Others believe was rebuilt into Ultra Magnus (a character who will debut in the Transformers movie, who Prime refers to as his "old friend"). However in 2010 Hasbro themselves gave an official answer: Dion is dead.

Errors

-Parts of Slingshot are colored black instead of red during this shot.
-The first lasers Skydive fires at Skywarp are colored pink instead of yellow.
-The top of Slingshot's head is colored white instead of orange during this shot. This happens throughout the episode. Like, a lot.
-The Autobot insignia on Prime's trailer is in the wrong place during this shot -it should be on the white stripe.
-Wheeljack briefly overlaps Ironhide when they start searching through the wreckage.
-Skydive says "huh?" when it should have been Fireflight.
-When the Aerialbots run back to the hangar, Aerial can be seen with them, but she shouldn't be there.
-When the guardian starts swinging Superion around, the floor is missing.