On the distant planet of Traal, the evil Deceptitran has enslaved a race of humanoid people called the Traalicons. They toil ceaselessly, building his city, while he sucks away their life force to make Energon cubes. The Traalicon slaves eventually rebel, and Deceptitran sends an SOS to the Decepticons on Earth. The Autobots intercept the message, not aware it was sent by Decepticons, and Optimus Prime sends Seaspray, Bumblebee, Cosmos and Perceptor to check it out. They arrive on the planet in time to help the Traalicons escape from Deceptitran's warrior drones. Seaspray meets up with one of the rebel leaders, a girl named Alana, and both are instantly smitten.
Megatron, Soundwave, and Dirge arrive on Astrotrain to aid Deceptitran. Meanwhile, the Traalicons lead the Autobots to the Well of Transformation, a mystical pool of water which transforms living creatures into whatever they wish. The Traalicons use its power to transform themselves into mer-people, though Alana warns the Autobots to stay way, as the Well is fatal to machines. The Autobots go a different route and meet up with the Traalicons in their secret underwater city. However, Bumblebee gets left behind in the escape and is taken prisoner by the Decepticons.
Seaspray and Alana sneak into Deceptitran's city to rescue Bumblebee and barely make it out. As Bumblebee escapes with the other Traalicons, Seaspray and Alana draw the enemy fire. They take refuge in the Well of Transformation, though Alana again warns Seaspray that the Well is fatal for machines. Seaspray wants to prove that he's more than just a machine and enters the Well. He emerges as a handsome Traalicon. Seaspray and Alana express their feelings for one-another, though Alana says she liked him better as a robot. The two then enter the well together and change into mer-people. As they return to the under water city, The Decepticons attack and begin to destroy everything. Seaspray and Alana escape, though Megatron sends Rumble to follow them. Rumble follows into the Well of Transformation and begins to change. Alana tells him the only way he'll survive is to think about a tree. Her ruse works, and Rumble transforms into a completely immobile tree. Seaspray emerges from the Well in his robot mode, and much to his surprise, Alana emerges as a robot, too.
The pair attack The Deceptitran's headquarters. Alana reprograms Deceptitran and has him send a message requesting help from Megatron. At the same time, Alana forces him to order all the warrior drones to attack The Decepticons. Megatron and his cohorts arrive and chase Seaspray into the Energon warehouse. The warrior drones then take them by surprise and attack, detonating the Energon supply. The explosion causes an earthquake which knocks tree-Rumble into the Well of Transformation, restoring him to normal. The Decepticons then retreat from Traal. The Traalicons celebrate their freedom as Seaspray and Alana boat-off into the sunset.