In desperation to get with the beautiful and popular Cleopatra, Abe Lincoln is hoping to make a move on her at JFK's party. JFK, however, also has the hots for her and will only let Abe come on the condition that he brings the beer. Meanwhile, Joan of Arc, who is trying to win Abe's heart, starts up a Teen Crisis Hotline in an attempt to impress him with her commitment to community service; their mutual friend, Gandhi, who accidentally agrees to help with the hotline, forwards the calls to his cell phone so he can go to the party. All the while, Principal Scudworth and Mr. Butlertron attempt to crash the party so as to better understand the students.
Cleopatra discovers she cannot continue to run for Student Body President because of term limits, so she convinces JFK to run on her behalf, and when Abe sees that Cleo appreciates leaders, he decides to run as well. But students of Clone High do not care about real issues, and many are infatuated with JFK; Abe employs a corporate sponsor, "X-Stream Blu," to jazz up his campaign. The only problem is that Gandhi becomes horribly addicted to this mysterious food product.
When Gandhi is diagnosed with Attention Deficit Disorder (A.D.D.), the students of Clone High begin to ostracize him. Abe must decide whether to please Cleo by doing the same, or to stand up for his "best dude 4 ever" and lose any chance of being with Cleo. Meanwhile, Joan struggles with living up to the legacy of her 15th century clone mother, and begins hearing strange religious voices in her head. Also, Principal Scudworth starts wearing Mr. Butlertron's sweater vest, in the belief that it gives him the power to relate to the students of Clone High.
When Abe decides to organize a Clone High Student Film Festival, he spends much time working on a movie about a misunderstood football-playing giraffe; Cleopatra stars in an autobiographical epic about how difficult it is to be as perfect and glamorous as her; Joan directs an avant-garde film which expresses her love for Abe through psychoanalytic dream imagery; and Gandhi and George Washington Carver work together to make a hilarious mixed-race buddy cop action comedy called Black and Tan. Meanwhile, JFK plans a film but never manages to leave the casting couch with his various wouldbe female co-stars, and Principal Scudworth starts to panic when his bosses on the Secret Board of Shadowy Figures invite themselves to his house for dinner, but thankfully for him, Mr. Butlertron is there to save the day.
The PXJTs are right around the corner, but Abe Lincoln is losing sleep running errands for his beloved Cleopatra. When Joan keeps trying to warn Abe about his sleep deprivation, a secret of hers is uncovered. Also, Gandhi, overwhelmed by the pressure of studying, decides not take the test and become a trucker instead. Mr. Butlertron and an old foe battle it out for the last time.
Since the CHHS basketball team refuses to allow girls or animals to play, the athletic Joan of Arc decides to cleverly disguise herself as "John D'Arc", becoming the star player. Cleopatra then falls for D'Arc, making team-captain Abe "Weakest"-Lincoln jealous. But Cleo's not the only one falling for John, as fellow athlete JFK finds himself having confusingly sexual feelings about the whole affair. Meanwhile, Gandhi and Genghis Khan kidnap the mascot of Clone High's rival school, Genetically Engineered Superhuman High.
Abe and Cleopatra's new relationship is threatened when she is picked to be on a Canadian Spring Break Dance show, hosted by Ashley Angel from O-Town. Meanwhile, Gandhi becomes an international rap sensation with the help of JFK as his manager. Also, Principal Scudworth is constantly being tricked by a pesky skunk.
Storm's-a-brewin' when Joan of Arc's house burns down and her family has no choice but to move in with Cleopatra's, where conflict ensues; Abe attends a Conflict Mediation Seminar to learn how to more effectively resolve disputes between the two. Gandhi and JFK find themselves in escalating arguments. Meanwhile, Mr. Butlertron becomes jealous when Principal Scudworth forms a relationship with a robotic toy dog.
After an anti-drugs assembly at the school, a rumor goes around that one can get high smoking raisins, leading the clones to embark on a musical, mystical journey of intoxication and irresponsibly long hair. Sober Joan of Arc is trying to keep Abe from turning into a drugged-out hippie, while Principal Scudworth and the PTA build a giant wall in an attempt to fence the students in. Also, Gandhi goes on a raisined-out subconscious mindtrip where he encounters a hummingbird-unicorn-donkey creature, a two-headed Olsen Twins monster, a talking Italian pencil, and a stereotypically Australian dragon, on his quest to rescue a princess who he believes will have sex with him.
JFK's long time best friend, Ponce de León, litterally dies, causing JFK to sink into a spiral of depression. This causes tension between Abe and Cleopatra, who dutifully attempts to comfort JFK, her former boyfriend, during his grief. Meanwhile, Gandhi is mistakenly sent to death row where he has trouble getting high fives, but makes new friends in the showers.
It's the politically correct Snowflake Day season, and everyone is in the holiday spirit, except for Joan of Arc, who is against the commercialism of the made-up holiday. But a homeless urchin who may be an angel or the pop sensation Mandy Moore teaches Joan an important lesson. Meanwhile, Abe and Gandhi attempt to invent and market an interesting device, so that Abe will have money to buy Cleopatra an expensive Snowflake Day gift.
With prom not too far away, Abe wants to ask his girlfriend, Cleopatra, but cannot stop thinking about Joan of Arc's prom date situation. Meanwhile, Gandhi goes on a desperate search for a date. So, Abe and Cleo each have a go at making over Joan for prom, JFK gives Gandhi a makeover, and Mr. B gives Scudworth a makeover to help him execute a sinister, evil plan to "win" the prom king vote.
As all the clones are preparing for the winter prom, Abe Lincoln decides whether to ask Cleopatra or Joan of Arc; Gandhi concocts a brilliant plan to get dates for all the school geeks; and Principal Scudworth attempts to execute his sinister, evil plan, while the Secret Board of Shadowy Figures prepares to abduct the clones on prom night to advance their own evil plan.