At the KND Moonbase, a graduation ceremony is taking place in the auditorium, with Numbuh 362 acting as moderator. The ceremony is for to welcome the Cadets Next Door, including Tommy, Sonya and Lee, into the Kids Next Door. Tommy is disappointed because his brother, Numbuh 2, isn't there to watch him. Numbuh 362 then says that they can't technically induct the Cadets into the superincredibly big computer-mabob and into the Kids Next Door because the Code Module was stolen (by Cree in SLUMBER). Just then Numbuhs 1 - 5 show up, battle-scarred, but with the Code Module in hand. The Code Module is quickly re-connected with the computer and they select Tommy to graduate first. To enter into the KND, he has to enter his genetic code into the Code Module. To enter a genetic code, one has to register their DNA with something unusual: boogers! Tommy places his booger into the Code Module and selects the codename Numbuh T. Everyone objects to T being a number, but after Tommy insists on using T, they decide to let him in anyway. He is assigned to Kids Next Door Sector V (the same sector as in Numbuhs 1 - 5). Tommy then starts making a speech about he had waited all his life for this day.
Unbeknownst to them, however, the KND are being watched by Father and the Delightful Children from Down the Lane from their mansion. Father says that Tommy had joined the KND just in time for its utter destruction. Father then proceeds to activate a machine, but then the power is cut off. Father goes to figure out what is going on and discovers that his own dog, whose name is Ben, started tearing out the wires. Father notices the dog and the dog runs off, but Father cuts him off with one of his weird abilities and then grabs his body to stop him from running off again and pulls him back -- it's a KND operative in disguise. Now really ticked off, Father starts advancing on him, warning him very sternly that he had just made a very big mistake.
Back at the Moonbase, the graduation ceremony is over and Tommy is going on and on about how he and the KND will be doing cool stuff together. Then suddenly, Numbuh 88's voice comes over the loudspeaker and explains that Father's device is operational. Numbuh 88 then says that "Father's got the..." but is then cut off and replaced by the sound of a rooster crowing. As if that wasn't bad enough, they then lose the signal. Numbuh 362 then calls the KND to scramble. The KND all rush off to various ships and vehicles and take off for Earth. They reach the DCFDTL's mansion and surround it. Then they launch a barrage of weapon fire against the mansion (first, lasers, then, missiles), but the mansion manages to fight off the KND's weapons (by putting up armor, protecting it from the lasers and by destroying the KND's missiles with some missiles of its own). Then the KND land on the ground and led by Numbuh 86, storm the mansion. Then some Knightamatons come out of all the doors in the mansion and go after the KND, who try to fight them off.
Back on Numbuh 362's ship, with Numbuhs 1-5 and Tommy on board, as well, they think that Father has turned his whole mansion into one big weapons system and Numbuh 1 says that it's probably a device that turns kids into adults. Numbuh 362 promptly assigns Numbuhs 1 - 5 to take out the device and they suit up in "birthday suits" to protect themselves against the aging ray. Birthday suits are special suits of armor that make one immune to the ray. But Tommy thinks Numbuh 362 meant the other birthday suit and is completely naked. Luckily, he has his pants in front of him to prevent showing his privates. But he doesn't have his own birthday suit yet. When she sees Tommy left, Numbuh 362 hastily leaves to attend to the troops. Tommy puts his clothes back on and feels unwanted.
Numbuhs 1 - 5 have penetrated the mansion and are making their way through. But they're being watched by Father via his security cameras. He instructs the Delightfuls to supervise the battle while he gives the KND his full attention. Unbeknownst to him, however, Tommy is also making his way through the mansion and he gets out of camera range just as Father looks back at the cameras, so he fails to notice Tommy. The KND meanwhile enter the same room as Father, who promptly uses his fire to melt their weapons. Then the doors lock, trapping the KND in and Tommy out. Tommy can only watch through a keyhole in the door. Father reactivates his machine and the KND put on their birthday suits to protect against any and all aging rays. But Father was too smart to turn them into adults, since they are annoying enough to him as kids. The ray appears and starts out as a small circle but gets bigger and bigger. The KND are engulfed in the ray and it reveals that the ray turns people into animals! The KND get hit by the ever-increasing ray and are turned into different animals. Tommy is traumatized by all this.
The KND operatives outside the mansion are still firing their weapons at the advancing suits of armor, but they just keep right on coming. Meanwhile, Tommy continues to watch the whole incident inside the room through the keyhole. He discovers the ray increasing in size. It even manages to go through the wall! Tommy retreats back through the mansion, passing the Delightfuls as he goes. The Delightfuls are engulfed by the ray, but it has no effect on them. Tommy learns that the ray affects only KND operatives. Tommy questions how the ray knows, but they just say, "Who cares?" The ray is still getting bigger until it covers the entire mansion. Now some of the KND operatives closer to the mansion are becoming affected and they all have no choice but to retreat and still the spherical ray is increasing in size and the operatives are still getting affected and now are turning into various animals. Numbuh 362's feet are caught in the ray and she too starts to change into a half-human, half-monkey creature.
The remaining KND members make it back to the Moonbase and STILL the ray is increasing in size. Pretty soon, the entire Earth is encompassed by the ray, which is STILL enlarging. It won't be long before it reaches the moon. The KND operatives quickly reconfigure their birthday suits to prevent being affected by the ray. As the ray continues to increase, the KND operatives (minus Tommy, who still doesn't have a birthday suit of his own) leave for Earth in their ships, entering the radius of the ray. Unfortunately, the suits only delayed the ray's effects on them. Now Tommy is the one sole member of the KND left.
Back on Earth, in the Delightfuls' mansion, the Delightfuls congratulate Father for his success. Father just orders them to go clean out the animal pens. The Delightfuls reluctantly leave while Father complains about children complaining about getting pets but not cleaning up after them. He notices they forgot the pail and the pooper-scooper and orders them back in to retrieve them and they come back... as sheep! Tommy then shows up and Father tells him what's up: the ray is able to distinguish between KND members and other people because of the Code Module. Father had deliberately allowed the KND to retrieve it after he changed it to uplink with his computer and the KND supercomputer. Since the Code Module connects to the KND supercomputer, and the supercomputer contains information about every KND operative, the ray is able to tell who is a KND operative. Tommy had quit the KND and made the Delightfuls members, which is why they were affected and he wasn't. Tommy then tells Father that the only way to reverse the ray's effects and change his children back to normal is if he turns the machine off. But in his fits of evil, Father refuses, because the Delightfuls are annoying to him and he likes them better as sheep.
Father then surrounds himself with fire and Tommy retreats and Father follows in hot (literally) pursuit. All the transformed KND then attack Father, but he manages to fight them off with his fire. But they do manage to stall Father while Tommy reaches a dungeon deep down inside the mansion and frees the caged transformed KND operatives. Father, now really furious, barges in and pins Tommy against a wall in one of the cells of the dungeon. But before he can send Tommy to meet his maker, Tommy jabs his finger up Father's nose and pulls out a booger and then places it in the Code Module (which Tommy had with him). Now that Father's DNA is in the Code Module, he's now an "official KND operative" and no longer immune to his own ray. As Father turns into a panther. Tommy escapes and slams the cell door behind him shut, locking Father in. Tommy then destroys the machine activating the ray, which causes the ray to die. The ray's effects die with it and the KND operatives are finally back to normal.
Back at the KND Moonbase, Numbuh 1 asks Numbuh 362 if there's any way to reinstate Tommy, but Numbuh 362 says they can't. Numbuh 4 then threatens to quit the KND, but nobody listens to him. The reason why they can't recommission Tommy is that when someone removes their DNA from the Code Module, he or she is forever excluded from the KND; it's a failsafe to prevent decommissioned operatives from hacking into their systems. Tommy says it's okay about not being in the KND and prefers working alone as "The Tommy". He then leaves for Earth in a spaceship made around himself. Numbuh 5 watches him go and comments to Numbuh 2 that Tommy definitely is his brother and they all burst out laughing. Numbuh 2 questions suspiciously what that means.