A boy admires a girl in his class until the bell rings. When he goes outside, three school thugs throw him into the dumpster. A moment later, he flies out in a Superboy costume. One of the thugs is about to attack him with a chain, but the boy uses his heat vision to burn the chain and to turn him into a pile of ashes. He blows the second thug into a vending machine and the 3rd thug runs in fear. The girl stands near, admiring him, then the alarm sounds and the boy wakes up from the dream.
The boy's name is Billy Hercules, a child genius, and TJ and Clark are going to his school for an interview. At school, Billy looks on as an older boy flirts with his crush. As class lets out, the teacher mentions a field trip to a naval base the following day. Outside, Billy runs into three bullies, similar to the thugs in his dream. Clark and TJ arrive and while TJ is distracted, Clark sees that Billy is in trouble. When Billy runs, Clark freezes the sidewalk, causing the bullies to slip and fall.
TJ and Clark find Billy leaving class, but he's tapped out on college interviews and declines. Clark finds him in the library and gets an understanding of his desire to be accepted by the other kids, despite his high intelligence. Clark relates with the boy, as he talks about being different and about getting his crush to notice him.
The next day at Langston Naval Base, an admiral explains their facility to the students while the class bullies taunt Billy. After everyone clears the room, Billy stays behind and watches as a seaman types in a password to the system. That night, Billy has the idea to get his crush's attention by tapping into the Navy's missile system and implanting a virus containing a poem to her. The next day, the admiral is explaining the launch of the vessel to the press, while Billy's class watches the broadcast from school. When they're about to demonstrate the missile system, the virus kicks in and sets off the alarm. Clark and TJ watch from the dorm as the computer reads Billy's poem. The class gets a kick out of it, but Billy has disappeared from his seat.
Clark leaves as he sees the submarine's chaos on the news. The missile system is about to launch two missiles, but has no target, so they'll self-detonate, lighting up the submarine and half the east coast in 30 minutes. The admiral puts the coast and armed forces on high alert, while at home, Billy frantically tries to deactivate the virus with no success. Superboy arrives in his room and asks for his help in killing the virus. Billy apologizes and will do anything to help and they fly to the sub.
When they arrive at the sub, Billy helps with the virus while Superboy tries to deactivate the missiles. But he can't go through the hatch without the access code, otherwise blowing up that section of the sub, so he uses his heat vision to burn a hole into the 6-inch thick hatch. After several minutes, Superboy's power begins to tire, but Billy has the virus figured out…..almost. It deactivates, but still denies access to the missiles.
Things are looking down and time is ticking, so Superboy orders everyone off the sub to a rescue chopper waiting outside. The lieutenant of the ship stays to try and crack the virus and Superboy goes back to burning a hole in the door until he sees Billy – he sneaked off the rescue chopper before it lifted off. He stays to help with the virus and Superboy works on the door once more. Billy has a terrifying daydream that the sub explodes and Superboy is hurt, but then regains his composure and continues finding the virus.
He figures out the virus and cracks it, deactivating the missile hatch. Superboy busts through it and disables the missiles with a fraction of a second remaining. Superboy leaves the sub in the lieutenant's hands and flies back inland with Billy. At school, Billy finally has the long-awaited attention of his crush, while the three bullies look along in bewilderment.