As the new school year beings, a few changes have taken place; Christopher has graduated and is moving on to unknown future, Miss Sherwood has finally published her novel and has moved to Maine, and Ian Ware has joined as a freshman but is discouraged when Mr. Shorofsky opts to retire.
Christopher's cousin is having a wedding with Jesse and Nicole set to dance as a couple. Nicole feels that things have changed and breaks up with Jesse but after getting back together, the two are unsure about where their relationship stands. Danny and Jillian start dating but her over-protective family smothers her.
After being reacquainted with an old actor friend, Paul Seeger, Lydia gets him a job as an acting teacher at the School of the Arts. His toughness isn't received well at first by the kids, but as he opts to leave, they have a change of heart. Danny is asked to give a tour to Hannah Cooper an 11 year-old prodigy who's unwilling to play for anyone.
On the anniversary of Leroy's commencement as a teacher at the School of the Arts, he's faced with accusations that he picked one student over the other for the lead because she was Black. Mr. Shorofsky and Ian butt heads on their tastes in music.
Jesse presents his 30's-styled play to Mr. Dyrenforth who decides to fund the play with hopes of obtaining the prize money of $20,000 from the Kimble foundation. The board decides not to supply the funds but Lou Mackie donates the necessary production money. All is well until Nicole, who plays lead comes down with Laryngitis.
Chris' sister leaves him with her 9-month old son Spike when she has an emergency and Chris is put through the ups and downs of parenting. Mrs. Berg leaves Mr. Dyrenforth to his own devices to attend her brother's anniversary and he learns how valuable she is. Nicole, Dusty, Reggie, and Jillian form a band which creates disagreements between the girls.
Reggie challenges conventionalism in order to help the homeless and ends up in a bit of trouble with Mr. Dyrenforth and the law. Dusty's father, Reverend Tyler, visits his daughter in New York but is determined to take her back to Colorado as he finds the school environment risqué.
Frustrated with not getting work as an actor, Danny goes to the cable access station to get his own show. While in the building, he walks onto the set of "Mr. Whacky's World" and gets a job playing Noodles. With expectations to remain Mr. Whacky's stooge, Danny's left conflicted. Dusty misinterprets Jesse's friendly gestures for a romantic interest.
When Tina comes to visit Leroy, he plans to make her a believer in the Christmas spirit. Between studying and working, he makes little time for Tina which leaves her despondent. Mr. Shorofsky is getting his tonsils removed and two kids sharing his room think he's Santa Claus.
Nicole gets the opportunity of a lifetime when she's invited to sing back-up for her idol Frannie Fortune but Nicole gets a quick lesson in the dog-eat-dog nature of the business. After Mr. Dyrenforth reveals that he's lonely, Danny, Jesse, and Leroy decide to boost his love life by advertising the principal with his plastered pictures all over the city.
After an eventful party, Miss Grant is frustrated to learn that Danny and Nicole have not shown up for an important rehearsal. That frustration turns to grief when they learn that Nicole was killed while being driven home by a drunk driver, Mickey Garth. With the school grieving, Jesse takes it the worse vowing to kill Mickey.
The School of the Arts has been selected as the location for director Jeff Stave's new film "Kittens Go to High School." Appointed student assistant to Mr. Stave, Jillian falls for him but reality sets in and it becomes clear that they can't be together. Maxie Sharp, the lead actress in the film enrolls at the School of the Arts.
Mr. Dyrenforth is due for appendicitis and the board elects Ms. Fleming to fill in for him. Ms. Fleming enforces a doctrine that prohibits singing and dancing in the hallways. Miltie, in an effort to finally do a good deed, dresses up as the Crimson Blade and anonymously performs various acts of heroism.
After rekindling her relationship with her high school fling, Lydia learns that her lover makes a living as a stock swindler. Ian becomes jealous when his father starts hanging around the school, and hits it off with his friends.
Lou's brother Duke shows up and Lou is anything but trilled. After hearing Chris sing, Duke signs him to do an album for him. Lou warns Chris about his brother's slimy ways but Chris thinks Lou is jealous. Mr. Seger is asked to supervise the newspaper committee but has to deal with Reggie and Maxie's constant arguing.
After receiving a violin from Bavaria that was originally sent to him in 1947 and after seemingly mystical occurrences take place at the school, Mr. Shorofsky reveals to the students the legend that explains the magic of the violin. The students, convinced of its magical powers, begin to fight over its possession.
Jesse gets the key to the school to catalog Shorofky's collection of sheet music over the weekend. Joe Mackey is hosting the Grand Gathering of Muskrats at his cafe and convinces Leroy to be initiated as a new member. Chris needs to learn how to cook so he can audition for the host of the cooking show "Macho Gourmet". When Miltie convinces Jesse to throw a party at school to raise money for repairs, what could possibly go wrong?
When Ian's old girlfriend visits him, feeling homesick and missing her, he decides to go back to England something to which she objects. Mr. Shorofsky wants to send Ian to a competition for classical guitarists and Ian openly objects. The gang prepares Lou for his campaign for President of the Metropolitan Bowling Operators Association.
When Danny's old friend comes to visit him, he surprises him with more than the news that he's working for Lou when he reveals to Danny that he's gay. Danny has an especially difficult time dealing with his friend's homosexuality. Leroy and Miss Grant compete with their choreography with a spot for the winner's routine to appear a stereo store's local commercial.
While typing up Chris' resume at work in a top secret company, Jillian accidentally sends top secret information to Chris' home address. Chris becomes the subject of a pursuit by two men traveling in an ice cream truck. Reggie, Ian, and Dusty take part in a student video contest but their subjects prove to be troublesome.
After helping her out when she gets kicked out of her English class, Reggie's close friend and the cafeteria lady, Rose, joins the school of the arts under Reggie's suggestion but when asked to audition with Reggie for a summer stock company, Rose gives up on both the stock company and the school but rekindles her passion for performing.
The National Cultural Center selects The School of the Arts to contribute an item to a time capsule to be opened a century later but no one is able to agree on what that item should be. When Mr. Shorofsky gives Miltie an ultimatum; write a song or fail, he tries to pass off a fourteenth century ballad as his own.
When Mrs. Berg learns that her old lover is coming to visit her, realizing that her lie of running the school has come back to haunt her, the kids help her pose as school principal. Gordon, a squeamish animal-loving student has difficulty in Chemistry class with dissecting frogs so he and Reggie try to convince Mr. Dyrenforth to approve a simulation computer program that provides the ability for virtual dissection.
The school is trying its hands at its first video yearbook and with alumni week in session, Bruno, Coco, Doris, Montgomery, Holly, and Chris are interviewed for the video. Miss Grant recommends Leroy for a lead in the alumni week show which is to be choreographed by big-time graduate Michael Taftner but he is not convinced that Leroy can take on the part. When Chris is asked to be guest speaker for Mr. Seger's class, he lies about his success which the two but heads over.