Nuclear Confusion is the second part of the 10th episode of season 2. In this episode, Dee Dee takes Dexter's power source for her lamp. However, she does not know that taking the core will cause a nuclear explosion. Dexter must return the core to its original spot before time runs out.
Dexter is in his lab testing his newest invention: A nuclear-powered lamp. Just after inserting the nuclear core, the test proves to be success. To celebrate, Dexter goes to get his favorite book titled Big Book of Brains. When he returns to the armchair, he turns on the lamp, but it doesn't activate. Alerted, Dexter frantically searches the lab to find why his lamp wasn't working. Suddenly, he finds a note written by Dee Dee saying that she hid the nuclear core. Realizing the damage Dee Dee made, Dexter follows the clues Dee Dee leaves behind to find the nuclear core before the meltdown occurs in one hour.
Dexter receives his first clue, then has Computer analyze it. She reminds Dexter of the equation Pi r squared (πr²) and the flavors apple, cherry, and blueberry being flavors. With this, Dexter runs to the kitchen to find three pies sitting on the table. With Mom's permission, Dexter eats all three pies and finds the next clue inside the pie pans, each of them saying "Go next door".
Dexter leaves his house and heads over to his neighbor's to find his touchy-feely neighbor waiting to greet him. She invites him inside and goes to get Dexter some cookies. Dexter peeks inside the kitchen and finds the next clue on the rump of the woman's pants: Dad's trophy. He races back to his house and heads to Dad's den to find his prized swordfish hanging on the wall. He slams the fish on the ground, jumps on it, and the swordfish spits out a piece of paper. Before he could go to the next area, Dexter hears Dad coming and hangs himself on the wall pretending to be the swordfish.
Just after Dad and Phil walk by, Dexter reads the clue and goes to Dee Dee's room to find the core. Once he gets it, Dexter is then chased out of Dee Dee's bedroom and back to his lab by a giant yarn ball. He throws the nuclear core back inside the machine and it settles down. Dexter returns to his armchair to find that his Big Book of Brains book has gone missing, with Dee Dee wanting him to follow more of her clues. Dexter yells her name in anger.
When Dexter's computer analyses the first clue, it reminds Dexter that "pi is r^2", but this is incorrect. The true point of the clue is that the formula for the area of a circle is pi multiplied by the square of a circle's radius (r).
After Dexter eats all three pies, he is seen laying on the table. In the next scene, he is seen on the floor. After that, he is then seen standing on a barstool.