Timmy's shot at the perfect attendance award is threatened by a pounding from Francis. Timmy wishes to become invisible and soon, everyone believes the school is haunted. Everyone that is, except Crocker who knows that catching the invisible Timmy will be all the evidence he needs to prove the existence of Fairies.
As Timmy is in his car on the way to school, he is excited to get a perfect attendance award that night. Unfortunately, when he reaches Dimmsdale elementary, he sees Francis and realizes that the bully is celebrating the end of school by beating up all the school boys outside. As Francis smashes a kid into the window of Timmy's car, Timmy gets his oblivious parents to drop him off literally inside the school to avoid getting pummeled. During class, Francis throws a note at Timmy, stating that he will die at half past nine. When the time comes, however, Timmy distracts him with a brick wall and makes a run for it, Francis following shortly behind.
After coming to a dead end, Timmy comes to the conclusion that Francis will only beat him up if he sees him, leading Timmy to wish that he was invisible and that Cosmo and Wanda would disguise themselves as school children. After noticing that Timmy has magically disappeared, Francis threatens that if Timmy doesn't return by the end of school, he'll beat up Cosmo instead. While Francis walks away after Timmy rips the bully's pants with scissors, Timmy decides to use the opportunity to cause mischief that leads the school into thinking it's the work of a ghost. Seeing these antics, Crocker correctly surmises that Timmy has magically made himself invisible, so Crocker then dons a heat seeking magic detecting suit to capture him and prove the existence of fairies. While Timmy dodges Crocker, he sees that it's half past five and hurries to the award ceremony.
Chasing Timmy into the school's kitchen, Crocker crashes into some bags of flour, covering himself with the substance. After the incident, Timmy is able to make his way backstage. Meanwhile, becoming afraid of Francis' threat towards Cosmo, Wanda poofs into a bat and uses her sonar to detect and find Timmy. After she is spotted by Crocker, she quickly turns into a baseball bat and beats him up, helping Timmy understand that it is wrong for him to run away and hide from his problems while his friends are out there fighting his battles for him. Timmy realizes that because of his cowardice, Cosmo would get beaten up and that isn't fair. Also, if he doesn't change back soon, he won't receive his award.
Timmy then wishes he was visible again, and Waxelplax then gives Timmy his perfect attendance award after raising the curtains up. Crocker then grabs him and tries to prove he is using magic while not realizing he's visible once more (due to him still wearing his magic vision goggles), making the audience mock him. Principal Waxelplax assumes that the flour-covered Crocker is the one that scared the whole school by assuming the identity of a ghost. A security guard then grabs Crocker, takes him away, and beats him up. Seeing Timmy, Francis confronts him and is shocked by his lack of fear. Timmy confesses he's afraid but states that he can't keep running away from his problems and is willing to face Francis.
Attacking him, Francis misses and punches Timmy's medal, hurting his own fist and leaving Timmy unharmed. Frustrated, Francis tries to use his other hand, his head, and even his spleen somehow, but only the tough medal gets hit, causing him to hurt only himself, leaving him to collapse on the ground in pain. As Timmy and his parents leave, Mr. Turner asks Timmy how his day was, and Timmy states that it was like he wasn't even there, and the episode ends as Timmy becomes invisible again.