At the start of the episode, Randy said "Chapter 2" as the title card appear when Howard interrupted him saying he barely survived the first chapter of chemistry saying he would wait for the movie and threw Randy's chemistry book out the school bus and it hit on a student as the school bus leaves. Randy then chided Howard for throwing out when Howard commented it was boring saying: "Chemistry:The Movie?" and said he hated the book, Howard then told Randy a booger story(which he described as the greeniest, the biggest, the juicest) in which Randy interrupted and replied he doesn't want to know and Howard said that he definitely want to know and as Howard told his story (the school bus that Howard and Randy were in was near a construction site made loud jackhammer noises as Howard told the story with some hand gesture) with him saying some parts as Randy making disgusted-based looks as he hear Howard's story. After that Randy told Howard he missed it with Howard saying he knew he would be sorry.
Randy asked Howard why he would tell all this stuff as the duo then entered the school in which Howard saying that they are best friends and should each other everything when Randy replied that they should keep some things to themselves when Howard suddenly laughed saying that he doesn't keep anything to himself. Randy said that he CAN keep anything to himself when Howard replied that Randy doesn't keep anything when Randy was nervous which Howard was shocked that his friend was keeping secrets from him.
Meanwhile, in Principal Slimovitz's office Principal Slimovitz was talking to someone who he saw aimlessly wandering the halls saying he's assuming that person would be the new teacher when the person said his name was Catfish Booray saying that he would be the new subsitute teacher when Slimovitz asked for his ID and Catfish gave him a turtle. After Slimovitz left, "Catfish" started laughing evily saying now that he has entered the school, he will be finding the ninja and started laughing maniacally as The Sorcerer laughing saying to the his rat friend saying it is the dawn of a new era when he said that when Catfish found one of his power balls, he became the his puppet when the rat asked how, in which the Sorcerer replied that Catfish would do anything The Sorcerer do when the rat asked how he do that, to The Sorcerer's dismay he did something ridiculous in front of the rat to prove it as well as Booray doing the same thing when Slimovitz came back seeing him jumping on the desk when Slimovitz replied that he had a good feeling about Booray.
Meanwhile, Randy and Howard entered their classroom still arguing about the keeping secrets issue, in which Randy replied to Howard that he's not telling him anything and Howard saying he WILL find out to which Randy wishing that there would be something to interrupt this conversation when suddenly Catfish/The Sorcerer entered Randy and Howard's classroom saying that he would be their new teacher when Randy immediately recognized Booray. To which Catfish/The Sorcerer asked how Randy knows his name, Howard then asked how Randy knows his name to which Randy angrily replied that he already knew how he know Catfish's name and that Catfish was the same crazy swamp wizard who tried to turn Howard into gumbos before, when a flash back of how Catfish tried to turn Howard into gumbos came back to Howard which he now remembers, when Catfish asked how Randy know his name which Randy replied that his name was on his armadillo, when Catfish said: "So, it is. Ha ha. So. It. Be." when Randy was curious to how Catfish doesn't remember him or Howard, to which Randy saying this would be okay.
Until Catfish finished writing his name and Randy notices his eyes glowed green Randy found out that something was wrong so he went shloomp in the Nomicon to found out answers when Howard took the opportunity to look through Randy's phone to see what secrets he's hiding while Randy being shloomped asked the Nomicon why Catfish is back, why didn't he recognize Randy and Howard, why his eyes glowed green and asked what are the qualification of being a substitute until the Nomicon explained how: Before his imprisonment, the Sorcerer's mighty orbs were flung to four corners of Norrisville. For 800 years, the evil orbs was not found until Booray finds one in his swamp. The Nomicon also said the spheres contain a terrible darkness, a source of unlimited power. After that, Randy then figured out what happened and vowed to find the power ball when Randy found out that he shloomped through the entire class when he noticed that nobody was there and raced out of the classroom.
Meanwhile, Howard at the bathroom looked through the last of Randy's email in his phone after finding out that Randy wasn't hiding anything and was determined to find out until he heard "Catfish" saying: "It's Ninja Poppin Time!" To which Howard overhearing Catfish/The Sorcerer conversation with his rat saying that the closer Catfish is to the Eye Of Eternities, the stronger his pull on him is. Catfish/The Sorcerer then summoned a power ball and swallowed it in order to lure Randy out to Howard's surprise. Howard then crawled down and through the other stalls in order to avoid being detected by Catfish as he transform(which he described as gross and disgusting as he crawled.) Once outside, Howard was about to tell Randy what he saw when Randy crashed into him and tried warning him about Booray when Randy replied he didn't want to hear one of Howard's disgusting story with Howard trying to tell Randy(with his mouth covered by Randy) about Booray until Booray himself (now transformed into a monster after swallowing the pearl) crashed through the bathroom door. After seeing Booray, Randy decided to transform into the ninja and went after Booray.
Booray,as a monster now rampaged through the school until he found the Eye of Eternities, with the Sorcerer conjuring his magic through the Eye, giving his magic to Booray by sucking up the power long enough for him to full strength, until Slimovitz showed up and started scolding Booray that substitute school teachers in Norrisville High turning into monsters are highly frowned upon, when Booray (in his full monster form) tried to hurt Slimovitz when Randy jumped in long enough to save him before Booray even attacked him, Randy then land a punch on Booray/The Sorcerer and then demanded for the pearl when Slimovitz replied that the school board won't forget about this, befoer fainting.
Then a fight was ensue, with The Sorcerer controlling Booray as the fight continued with Randy, before he even counter attack, hit by Booray's monster form's tail, trying to figure out how to de'stank him until Howard tells him Booray isn't stanked while holding a armadillo that Booray was carrying earlier on eating the eaten up apple. Randy asked how Howard knew all of this when Howard started taunting him that he shouldn't say about his secrets until Randy grabbed Howard with his ninja scarf asking how he knew to beat Booray, with Howard asking what secrets is Randy keeping, with Randy saying "I'm am not, not telling you anything." Howard then angrily replied saying the same thing Randy told him. Randy, finally fed up, started saying that there are some things he kept from Howard with him(Howard) happily saying that he knew that Randy was keeping things. Before he knew what, Randy, finally impatient, told Howard he promise to tell him everything later, asking Howard how to tell how to beat Booray saying that he(Booray) ate a giant glowing ball(Chaos Pearl), also adding that the closer Booray is to the Eye, the more powerful he gets. Randy figuring out how to beat Booray by knowing that if he lured Booray from the Sorcerer, Booray will lose all his power. After that, Randy started to lure Booray out, with the Sorcerer losing his grasp of Booray. Booray, now not controlled by the Sorcerer, continued to attack Randy. Being confused, Randy found that the Pearl was still inside Booray's stomach, tried to make spit out the Pearl using his scarf which it didn't work when suddenly Randy remembered about Howard's story, tried doing the same thing with Randy asking the bus driver to drive to the construction area(just like earlier there were construction noises), Couldn't take it, Booray spat out the Pearl and changed back, confused, wondering where was his swamp, with Randy telling the bus driver to "Hanga Left!" and Booray was thrown out to his swamp, saying "Oh, there's the swamp go! Never Mind!" Randy, now with the pearl, smoke bomb out of the bus.
Back at Randy's home, Howard was shocked that Randy used his booger story, with Randy commenting that it was disgusting with Howard saying it was epic, not before Randy saying that he has to prevent the pearl from falling into the wrong hands. Howard then asked what secrets has Randy been keeping, with Randy telling that sometimes, in the right, his sister was pretty spicy. After hearing it, Howard started saying he doesn't feel good, with Randy continuing saying about Heidi that made Howard more disgusted, saying he doesn't want to hear anymore, right before the scene turn black.
- The title of this episode is a play of the 1970's sitcom Welcome Back, Kotter.
- This episode is the official start of season 2's run.
- Clips from "Swampy Seconds" and "Randy Cunningham: 13th Century Ninja" appear in this episode.
- The first shot of the episode shows a page saying Chapter 2, which probably references that this episode is the start of season 2.
- The Messenger has his first important appearance since "Last Stall on the Left" by driving the bus while Randy and monster Catfish Booray fight on top.
- Randy has a new school bag in this episode.
- Randy admits that he thinks that in the right light, Heidi is very attractive. However this may have been to annoy Howard and to teach him a lesson.
- Randy's room is new design in Season 2.
- This marks the sixth time Randy has cried. The first was "Monster Drill", the second was "Bash Johnson: 11th Grade Ninja", the third was "Rise of the Planet of the Robo-Apes", the fourth was "Ninja Camp" and the fifth was "McFear Factor".
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