While rummaging through the local junkyard for parts that might be useful to Donatello's penchant for building whacky inventions, the Turtles witness the crash landing of an alien spacecraft. After a debate as to whether or not they should investigate, they go inside and encounter an alien kid named Quarx.
Meanwhile, in another part of the junkyard, another alien spacecraft descends. Drako, a star trooper, emerges and reports to his employer that he has located the Starchild. His employer tells him that the "fleet" will be in position in two hours and to "handle the situation" until then.
Back at Quarx's spacecraft, the Turtles try to learn why the little alien kid is all alone, but Quarx would rather play than talk. And while he begins to play in the garbage, Drako arrives on the scene blasting away.
The Turtles successfully, but only temporarily, restrain him long enough for Drako to tell them that the Starchild is the "most dangerous being" in the universe.
Back at the lair, the Turtles discover that Quarx possesses telekinetic powers as he demonstrates them, first with Michaelangelo's Bugman toys, and then with Splinter's collection of ninja weapons - the ones with sharp blades.
This action does not sit well with the Turtles and they try to impart some parental authority, which of course only serves to bother the little alien, who insists that all the wants to do is play. He then runs off telling the Turtles that he does not have to listen to them - they are not his fathers.
While the Turtles try to track Quarx down, as he wreaks havoc all over town, Splinter decides to pay a visit to his spacecraft in hopes of learning more about the celestial traveler.
Meanwhile, Drako has returned with reinforcements, determined to "nail that Starchild." After being thwarted once again, Drako implores with the Turtles that they must let him "find the Starchild or their whole planet could be obliterated." But still the Turtles refuse.
Moments before the end of act two, Donatello announces the prescence of thousands of alien spacecraft orbiting the glove. Drako's employer leads this armada and he demands that the Turtles turn over the Starchild within thirty minutes or they will destroy Earth. And once again the Turtle refuse.
Drako explains to the Turtles that they wish no harm to the Turtles or their planet, but that the Starchild is very dangerous and that he has destroyed many worlds in the last two centuries. The survivors of these worlds have banded together to hunt the Starchild down to prevent him from destroying another innocent civilizations.
The Turtles are confused. How can the Starchild still be a kid after two centuries. Drako explains that the Starchild is very powerful and can be whatever it wants to be.
Back at Quarx's spacecraft, Splinter locates a video journal recorded by Quarx's father, Merrick. Merrick's journal details a civil war on his planet and the powers that he bestowed upon his son to end the war. However, Merrick's planet was destroyed before Quarx could learn about his father's gift to him and has "refused" to grow up without his father's permission.
Meanwhile, Drako has decided that not only does he want Quarx, but more importantly, he wants Quarx's power so that he can rule the Universe. He will not let the Turtles prevent him from having it.
After a failed attempt to take possession of Quarx and his power, the Starchild gets really angry and is about to use his power to destroy everything around him - that is until he hears his "father's" voice.
Using his ninjitsu mind powers, and a clever disguise, to "transform" himself into Merrick, Splinter tells Quarx, in a fatherly way to grow up and use his power to end war and create peace among the galaxies. And lo and behold, Quarx evolves into an adult, repairs all the damage he has caused on Earth and promises to make amends throughout the galaxy.moreless