Season 1

1. More Than Meets The Eye Part 1
With their energy reserves dwindling, the Autobots set out to find new reserves in their ship, the Ark, but are followed by the Decepticons who attack the Ark in a meteor shower. They board the Ark and in the battle which ensues, the Ark is damaged and thrown off course to crash land on Earth. Several million years later an eruption of a volcano causes the computer to reactivate and its repair program kicks in, repairing the closest Transformer to the specifications on Earth vehicles gathered by a probe. That Transformer happens to be a Decepticon who moves his fellow 'cons into the repair beam. They leave the Autobots behind and prepare to raid the world's resources, but Starscream unwittingly causes the Autobots to be reactivated. Some Autobots track down the Decepticons' base, but are discovered and barely escape. The 'cons attack an oil rig manned by humans Spike and Sparkplug Witwicky, and when the Autobots arrive, they and the humans are caught up in the destruction of the platform.

2. More Than Meets The Eye Part 2
The Autobots escape from the rubble and save the humans. Spike and Sparkplug return to the Ark with them to help them in their battle. The Decepticons continue to plunder Earth's resources and make Energon cubes, planning on returning to Cybertron with enough energy to lead the Decepticons to victory. The Autobots intervene, but are not able to stop the 'cons plot. In an attempt to trap the 'cons in the cave they are mining in, Bumblebee and Sparkplug go in to set an explosive device. They run into problems and Prime send Roller in to help. The device goes off, trapping Bumblebee and Sparkplug and injuring Prime through Roller.

3. More Than Meets The Eye Part 3
Bumblebee and Sparkplug are quickly rescued, but the Decepticons are able to blast their way out. Hound and Prime come up with a plan to trick the 'cons. The captured Ravage is allowed to escape, having overheard the location of a rocket base. The Autobots await the Decepticons attack at a holographic rocket base generated by Hound. The 'cons arrive, but Megatron anticipated the plot and the 'cons are actually dummies, with the real 'cons attacking the real site. The Decepticons have built a new ship to take them back to Cybertron, but they are ultimately stopped by Mirage who has stowed away on the ship and the ship crashes into the ocean.

4.Transport to Oblivion
The Decepticons, working out of an undersea base created from their crashed ship, create a "space bridge" back to Cybertron. Bumblebee and Spike are caught spying and are to be used to test the device which has already failed to work once. Bubmlebee is reprogramed to lead the Autobots into a trap, but Megatron must call his assault on them off when the space bridge is reactivated and must be used in only a short period of time. Spike is saved by Bumblebee, and the energon being transported is detonated, throwing Megatron into the bridge as it is activated.

5. Roll For It
Megatron returns from Cybertron. The Decepticons try to steal an antimatter formula which is given to a wheelchair-bound computer whiz named Chip. Chip ends up becoming one of the Autobots' human friends.

6. Divide and Conquer
The Decepticon jets badly damage Optimus Prime in an attack on a power plant. Several Autobots must go to Cybertron to obtain a part needed to repair Optimus. The Decepticons attack while the Autobots are thus weakened, but Prime is repaired at the last minute and answers Megatron's challenge for a one-on-one combat. The 'cons are defeated and retreat.

7. Fire in the Sky
The Decepticons are plotting to drain the Earth's energy through a crystal at the North Pole. They discover a Transformer, Skyfire, buried in the ice and revive him. He is initially allied with the Decepticons and his old friend Starscream, but when he sees how Megatron treats his human prisoners he joins the Autobots. The Decepticons are defeated, but Skyfire ends up frozen in the ice once again.

8. SOS Dinobots
The Autobots discover fossilized dinosaurs in their cave and it leads them to creating three Dinobots to help them. They are, however mentally unstable, and Primeorders them deactivated. When all the Autobots are captured by Megatron, Wheeljack goes against PrimeUs previous orders and reactivates the Dinobots. They save the others and prove their worth.

9. Fire on the Mountain
The Decepticons plan to use an ancient crystal as an energy source for their new weapon. With the help of an unthawed Skyfire, the Autobots are able to stop the Decepticons and restore the crystal to its rightful place.

10. War of the Dinobots
The three Dinobots get out of the Autobots' control and ally themselves with the Decepticons. The Autobots design two more Dinobots to bring the others back into their control.

11-13.
The Ultimate Doom Part 1
The Ultimate Doom Part 2
The Ultimate Doom Part 3
Megatron plots to bring Cybertron into Earth's orbit, and harness the resulting destructive energy. With the help of a human scientist, he plans to use hypnotised humans to assist him. Sparkplug is captured as a guinea pig for the experiment and he himself is the one to press the button bringing Cybertron into Earth's orbit. The Autobots combat various natural disasters on Earth, and journey to Cybertron to rescue Sparkplug. While there, Wheeljack develops a countermeasure for the 'hypno-chips' which are making the humans serve the Decepticons. On Earth, Megatron's ship, loaded with energon, is destroyed by the Autobots; the resulting explosion is powerful enough to push Cybertron out of orbit, although Megatron survives.

14. Countdown to Extinction
Both the Autobots and Decepticons recover from the aftermath of Cybertron's proximity to Earth. Megatron returns to lead the Decepticons. Starscream breaks into Dr. Archivil's lab, and connects the exponential generator there on a timer, which will cause it to explode and destroy Earth. He then travels to Cybertron, where he will collect the released energy. Megatron and Prime, warned by Shockwave, team up to stop the explosion; Starscream returns to find out what went wrong, and is dragged away by a none-too-pleased Megatron.

15. A Plague of Insecticons
Both the Autobots and Decepticons move to investigate the appearance of several new Transformers, the Insecticons. The first battle is between Skyfire and the Insecticons. The Decepticons form an alliance with them, and steal oil from a refinery. The Autobots intervene, but are seriously damaged by the lightning bolts shot at them by one of the Insecticons. They realize that if they transform they are insulated from the electricity with their rubber tires and defeat the Insecticons. The Decepticons and Insecticons end up turning on one another.

16. Heavy Metal War
Megatron has built the Constructicons to create a machine capable of transferring all the Decepticons' special powers over to him. He then challenges Prime to a fight which he must accept by a code of honor. Megatron defeats Prime, and the Autobots must keep their side of the bargain and abandon Earth. Meanwhile, the Constructicons have broken into the Ark to deactivate Teletran 1 before it can reveal that Megatron has cheated. They are confronted by the Dinobots and, even as Devastator, are defeated by the Autobots once they discover the truth. The Decepticons are all driven into a chasm.

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