A Befuddled Mind is the 10th episode in season 2.
Jake and Trixie are studying hard in preparation for their standardized test for school tomorrow, while Spud is too busy practicing as a mime, after being convinced by his Guidance Councilor that his recommended of being a street performer after reviewing his academics. Jake and Trixie are discouraged by Spud's lack of focus on his exams, and wants to help Spud practice his mind by helping him succeed in the standardized test for tomorrow.
At school, when the exams are distributed, Jake swaps his test papers from Spud for him to answer, then Jake changes the name of his paper to Spud's and putting his name in the test paper Spud answered. When it is passed, Rotwood's correction machine received Spud's supposed paper and revealed it to be a perfect score, Rotwood is utterly shocked and even tries to recheck it over and over again.
Suddenly, an agent arrives who reveals to be in association with the Manhattan Genius Institute (MGI) where Spud's perfect standardized test paper reveals to be government issued, and he is invited to join the institute of young geniuses.
Fu Dog also arrives unexpectedly and informs Jake of a dragon emergency, the gang ventures to the sewers after a sewer stroll informed Lao Shi that someone had stashed a powerful magical artifact and their mission is to retrieve it before it is possessed by the wrong hands. While searching, Spud is outraged after what happened during class, and is reluctant to go to the institute as he learned after being a genius his life will all be hard work and no time to cut loose. Fu Dog then finds the artifact inside a sewer pipe and Jake retrieves it, of what appears to be a purple container for the artifact. Suddenly, the now powerful wizard, Eli Pandarus arrives to stop them from retrieving the artifact. Eli summons troll minions to fend them off, Jake tries his best to defend but is unable to stop Pandarus from stealing the artifact from Trixie and dissapears.
At Lao Shi's shop, Lao Shi reveals the artifact to be as Pandora's Box, where unspeakable and unimaginable horrors are locked within inside the box. The gang concludes that Pandarus is one of the descendants of Pandora, the only people that can unlock the powerful box. But they can't figure out why Pandarus didn't open the box when he had the chance, to get it over with and continue his goals for world domination. However, Spud won't be able to help the investigation, as he has to attend his first day at the Manhattan Genius Institute, leaving Jake and Trixie to discover it themselves.
The next day, Jake and Trixie follows Spud of going to his Institute where they wish him good luck, but Spud is deeply upset of his new life and Jake suddenly feels sorry for him. On his first day, he still acts as himself and also practicing as a mine, where everyone else is focused and determined to improve and show their knowledge. Meanwhile, Jake discover's that the magic box is concealed by an enchanted box of which Jake concludes that the reason Pandarus didn't open the box, is that he hasn't figured out how to unlock it, but both of them still miss Spud to hang around with.
Back at the Institute, the genius students are competing against each other to show off that they are smarter, but Spud is relaxed and even reveals a few of the students that he intends to purposely fail all of the examinations, so that he can be kicked out of the Institute, the other students cannot allow that as it is against their nature of being a genius. The teacher then continues on handing out tests for the students, in which Spud quickly fails it all. The teacher tells Spud that if he fails the last test, he will be immediately kicked out.
Meanwhile, Jake and Trixie have no lead of Pandarus's plans to unlock the box, as Spud is not around to help them with. Fu Dog comes up with an idea to find and talk to Pandarus's former sideckick Monty Hall, who is in a bar in Magus Bazaar. Monty Hall is depressed after being fired yesterday as Pandarus's sidekick, Monty reveals that after he was fired, Pandarus took over the Manhattan Genius Institute by himself after his top researchers and scientists have failed to crack the code in the enchanted lock in Pandora's box. Pandarus then suggests he tries younger intellectuals to see if they can figure out the combination to the lock, when someone achieves it, he intends to later 'dispose' the person who figured it out. Realizing that Spud is in danger, Jake and Trixie quickly head out to the Institute.
Meanwhile, Eli tells the teacher of the Institute that if she fails to find anyone to break the code, she will remain to be a frog for the rest of her life. The teacher swore that she will not let Eli down and gives out the final exam, which is the unraveled code of the box, where the students' mission is to figure it out. Hours have passed, and most of the students have surrendered to continue to unlock it, but Spud still remains. The teacher feels his a waste of time, and recommends that he lives now, but after being mocked by the geniuses. Spud tells them that he only wants to balance work and fun, but one student wants him to prove it that he has intelligence. Spud agrees, and gives out his theory to the code where he deciphers it easily. Eli suddenly appears and kidnaps Spud for him to forcefully tell him the key to unlock the artifact.
Hours later, the Institute is now heavily guarded, Jake and Trixie luckily manages to stealthily sneak inside Pandarus's institute. Meanwhile, Pandarus forces Spud to tell him the combination to the lock in which so he does in fear, and now intends to get rid of him. Luckily, Jake and Trixie intervene but Pandarus's powerful magic overpowers them, Trixie manages to fend him off temporarily causing the wands that unleashes giant magical hands to seperate from him. Spud, then later manages to break free and grabs Pandarus's wands. After a few mistakes, Spud uses the same ability Pandarus used with his wands against him, pinned down by the fight. He gives up and dissapears, the trio happily reunites and embraces each other.
The next day, Jake and Trixie see Spud with his classmates from the Institute to teach them how to have fun, furthermore, Spud admits to Jake and Trixie that after answering the code of the lock, he likes the feeling of being challenged and that he wants to improve his academics. Jake and Trixie appreciate taking a bit of change in his life only until, that after he quits being a mime he wants to be a one man-band.