The students fear getting vaccinated, resulting in Nurse Gazelle using a blowpipe to inject them. Unfortunately, she accidentally hits Adam with Jake's inoculation; he seems fine at first, but ends up regressing into a dumb ape.
A high score in the school placement test puts Adam in the honors class where he is teased by the students at first, but he is soon respected by them when they see his excellent spelling skills.
Coach Gills teams Adam and Jake as one player for the Charles Darwin middle school football team when Adam displays excellent memory at the game play and Jake displays his good arm for tossing.
After Adam and Jake break a fish tube, Jake's consequence is to work in the school office filing papers, while Adam's punishment is to guide an endangered panda, Dingbang, around the school.
After Adam complains about the cafeteria food, Principal Pixiefrog replaces the animal food with human food which causes the animals to get fat from the unhealthy human foods that are supplied.
Jake is offended after Adam describes someone "going ape" so Adam tries to make up to Jake, though Jake keeps refusing the apologies.
When Adam accidentally hits resident Bull Sharkowski's snout, he is dubbed as the new school bully.
Mrs. Chameleon thinks that Jake should have the role of Jungle Guy (a parody of Tarzan) but Adam wants the role also.
Slips is shedding his old skin but everyone thinks it is a virus he is spreading around the school called the AAACCCK.
When Jake finds a diamond doorknob, he discovers its power when all of his classmates (except Adam) become enchanted with the item due to its shining, causing Jake's obsession of his butt to go to far, making all of the students study only monkey butts.
The star of the self titled "Amazon Kevin's Wild Animal Takedown" comes as a surprise at the invitation of Adam to the school, though the animal students dislike him due to his roughness towards animals on the show.
There is a textbook shortage and to raise money to buy new books, Adam and Jake try to sell selling chocolate-covered grubs during Charles Darwin Middle School's Annual School Sales Drive.
After receiving a number of citations, Adam and Jake are put on Hall Monitor duty, and Adam discovers the corruption of the Hall Monitor students.
Jake becomes the school's class clown after his talking buttocks routine is a success.
On Howloween, Adam goes into the living room to get a file for Principal Pixiefrog, and discovers the ghost of an old human janitor. The show are back at CDMS News.
Jake makes up for semi-intentionally ruining Adam's science fair project by implanting a robotic arm in his skull that starts to have a mind of its own.
Adam and Jake discover unsent love letters to Mrs. Tusk by Mr. Hornbill, and they decide to coach him to ask Mrs. Tusk out on a date.
Zira Cornelius, a famous documentary filmmaker, comes to Charles Darwin Middle School and focuses on Adam, believing him to be an unknown species, unknowing he's a human boy with a zit, swollen nose, and muddy clothes (due to a bad start that morning).
Adam is celebrating his birthday party at a pizza palace, but when his human and animal friends both show up, he has to find ways to keep them apart or else will be embarrassed.
Adam befriends a koala named Deidre out of pity, who turns out to annoy him as much as she annoys everyone else.
Adam enters the school elections and faces off against seemingly powerful Bull Sharkowski.
When Charles Darwin Middle School is closed due to bat guano contamination, school is held in a portable classroom. Problems start when Jake accidentally snaps the brake and the portable classroom wheels across various places.
After being played around by three lions, Adam tells the nurse he is allergic to some of the animals. Principal Pixiefrog puts Adam in a plastic bubble, and it becomes the latest fad at school.
Adam's excited when Kerry invites him to play paintball early the next morning, but can't sleep when Windsor, Jake and Slips show up for a sleepover.
Adam wants to ask Kerry to the school dance; Jake is shocked Adam doesn't want to go with him, and Ingrid thinks Adam wants to ask her to the dance.
Mr. Mandrill suggests that Adam and Coach Gills switch roles for day after Coach Gills loses her temper over Adam's performance in her class.
Adam and Jake take an aptitude test, but they are not happy with their results. So they try to find their true destiny
The Charles Darwin Jungle Squad wants Adam to cheer with them at the extreme cheerleading finals after one of the cheerleaders gets injured.
After Jake dumps a chum bucket on Principal Pixiefrog and thinking he and Adam did it, he gives them Saturday detention, only for Jake to do his basic cable variety show, Basic Jake.
Adam gets to go back to his old school as part of an exchange program. However, the school is not exactly the same as he remembers it.
In the refrigerated part of the school where students are taking their polar classes, Jake falls in with a bunch of "cool kids" and forgets about his other friends.
Henry's singing is very poor, but when Jake hears it, he mistakes it for talent and enters him in the talent show.
Jake wakes up with what appears to be a large, bushy moustache and it changes his life as he assumes he becomes a "man" by having it.
No one is reading the school newspaper and it is closing down. So Adam suggests that they write an interesting story. Trouble starts when Jake publishes lies about Adam. Things get edgy when Adam publishes Jake's secret.
When the school gets sued, Principal Pixiefrog takes time off from work. His replacement is Principal Wolverine, a principal (who is always shown squinting) who is making things miserable for the students, and even Ms. Warthog. Plus, he has an obsession with biting people on the butt, saying "Do I have to bite you on the buttocks?" as a threat towards students. So Adam and Jake attempt to persuade Principal Pixiefrog to come back to his old job.
When Adam tells Margaret Rhino that she is rare, she becomes so arrogant that her friends, Joanie and Latanya, get angry at her. But when Adam learns the truth about Margaret, he tries to tell them and has no choice but to take all three of them to a date.
After finding a stranded fish, Adam is granted a magic fish wish. Adam thinks this is nonsense while his friends want him to use the wish on them.
Adam, Jake and other students are given eggs that they have to take care of for a school assignment. Of course, Adam gets stuck doing all the work for Jake, and finds that this responsibility is too much for him.
Jake gets clones for himself and Adam, but are mean jerks. They are ruining their records/reputations by running around the school naked and causing chaos.
Jake takes a day off from school by spending it at school as part of his typical Jake fashion. He enjoys the facilities and persuades Adam to join him.
Lupe falls in love with Orlando Parrot, a parrot who is Jake's friend, who usually calls her "pretty bird", but finds out that he doesn't actually like her at all.
Animas is a celebration for animals and their instincts and Adam must hold himself up or he'll ruin the holiday for everyone. Also, Coach Gills is not enjoying Animas at all, with spoofs of many holiday specials such as How the Grinch Stole Christmas and It's the Great Pumpkin, Charlie Brown.
When the carnival comes to the school, Adam tries to win a princess ballerina snowglobe with opposition from the cheating Spiffies.
Adam is given the keys to the Lookout Tower after passing a safety test the first try. The Lookout Tower is a bachelor pad located atop the school. Adam's job is the look out for threats in the school, but his job is made difficult when his friends use the lookout tower to throw a party.
Instead of letter grades on his report card, Adam receives generic positive symbols. He complains about this to Principal Pixiefrog and he changes the current system to letter grades with terrifying results.
When Adam fails another Feeding Frenzy exam, Mr. Hornbill thinks that he may be held back if he doesn't pass the next exam. So Adam gets a tutor to help him, but the tutor is actually Bull.
Adam is embroiled in a prank war that he doesn't want to be in.
Teddy Truman, Windsor's ventriloquist's dummy, is enrolled into Charles Darwin Middle School. Most students think that Teddy is a living thing, except Adam.
Principal Pixiefrog institutes a school uniformity policy, which causes the students to act overly "proper" except Adam. Adam teams up with Dickie to return the school back to its old, less mannered ways.
Jake wants to join the space program, but the only problem is that astronauts wear pants and he detests wearing pants, so Adam tries to help.
Whilst Adam is off school pretending to be sick, Jake misses him to the point of mentally breaking down.
Jake tries to warn Adam not to fall for the Petting Zoo Kids' dirty tricks, but after falling for their cuteness, such as petting the lamb, rubbing the goat's belly, and hugging the pony, the little animals are robbing him of his dignity and his money.
Adam joins his friends for their annual field trip, but disaster strikes when the bus crashes, and members of the group are lost in the woods and unable to find their way home.
After borrowing a pencil from Phineas Porpoise, Adam and Jake have to deliver a lunchbox to a locker in return.
An Italian hermit crab named Herman finds a new home in Adam's locker, annoying him. Meanwhile, Jake searches for the legendary "Mermonkey".
Lupe becomes outraged when she sees that a toucan star is making her species look like idiots, Adam debates to end this conflict by creating the "United Species", an animal version of the United Nations. Meanwhile, Jake comes up with a plan to shut down the organization after getting kicked out
The laws of nature says that everyone must have a sidekick, and that sidekick must respect their leader, and Adam and Jake argue over who is the leader and sidekick switching every other duo in the school's respective roles.
Windsor tries to hide from Deb, a gorilla from Cameroon, because he is afraid that he will have to marry her.
Jake trades places with his spoiled cousin Lord Saucypants who is actually the pet monkey of minor popstar Dobie Broadway Jr. but his life is not as great as it sounds.
Everyone except Adam runs scared when thinking that a new student is actually an alien from outer space. They were correct. Note: This was chapter three in the story line of "Cartoon Network Invaded".
Principal Pixiefrog's ego becomes over-inflated when he wins Principal of the Year.
Jake fills in for Principal Pixiefrog after he loses his voice and bases his morning announcements on shock-jock style morning radio.
Adam gets a job in a gorilla costume to but is surprised when his friends find it offensive to the primates.
Jake has a crush on the substitute teacher, Mrs. Slender loris.
The gang must rescue Slips after he oversleeps in class and is stuck in night school.
Pixiefrog fits students with Citronella collars that keep them in line after finding Jake has "the gift", enabling him to see into the future and causing the other students to panic after foreseeing "the end".
Slips and Carl Mongoose become friends, not realizing that they are supposed to be enemies. After a film explains they naturally are predetermined to do so, they end up being enemies much to the annoyance of Jake and Adam.
Slips decides to become a guidance counselor, but learns that there is only room for one at CDMS.
Ingrid befriends Lola (voiced by Sarah Hagan), a llama who covets her life. Ingrid soon realizes that Lola is trying to steal her life!
Mr. Hornbill arrives at school with an insulting oxpecker bird on his horn (voiced by Lewis Black).
A cheetah takes jurisdiction of Coach Gills' job. Adam and Jake persuade Gills to get it back through a contest.
When the Polar Wing of CDMS starts to melt due to the effects of global warming, the entire school becomes flooded.
Adam's new cologne literally attracts all the girls, (animal girls that is) but when it falls into the wrong hands, Principal Pixiefrog is turned into a human after Adam hugs him.
Jake decides to take Adam to the zoo after school so he can meet his parents.
Jake's obsession for looking at his own butt goes too far. Note: This episode was banned from showing on Cartoon Network after its second time airing in early September 2007. Cartoon Network's new Executive General Manager (out of Atlanta) pulled the episode after he found it offensive and "too-butt-filled", which was deemed inappropriate and vulgar for the intended audience of children. Shortly after its removal it was nominated for an Annie Award in Writing. However, despite the episode being banned, it is still available through DVD boxsets, iTunes, Amazon Instant Video, Netflix and other online streaming sites and services.
Because of the Duck Boys Mulligans' misbehaving antics, Bull Sharkowski's water headphones fall off and end up in possession of Soupy the Basking Shark.
Adam hurts a hyena named Rufus's feelings, causing his laughing habits to come to an end.
Henry moving back to Greenland, which CDMS protests.
Adam joins an after-school club for tough feral cats.
Adam and the CDMSkids try to help Miss Chameleon overcome stage fright.
In a familiar clerical mixup, Jake gets transferred to Creeping Broad-Leaf Sedge Middle School, a school for plants.
Principal Pixiefrog is replaced by a robot, and eventually the entire faculty is replaced by robots.
Windsor starts to find fame when Adam makes a painting of him.
After going through a growth spurt, Ingrid feels that she is too tall for the halls and is sent to high school.
The gang goes to Hawaii for spring break while the faculty stays at school to welcome migrating birds.
When Virgil "Bull" Sharkowski comes to Charles Darwin after an orthodontist appointment, Adam and Jake notice some changes. Bull's braces are gone, and his personality has completely changed. Now he's no longer bullying other students and wants to give helpful advice to others.
Windsor feels both threatened and creeped out by the fact that his single mom is dating Mr. Mandrill! Despite Mr. Mandrill's attempts to reach Windsor and show him how much they have in common.
Jake's plan to join the school's swimming team ends badly.
After a secret is out about Nurse Gazelle, Principal Pixiefrog becomes the school's nurse.
Today is mid-terms at Charles Darwin Middle School, and Adam actually manages to pass all his tests with flying colors. But all the studying and preparation he had to do for the tests has put a strain on Adam's brain, and now he can't stop acting wild!
Adam discovers that Jake has bad eyesight and knows that his friend needs to get his condition treated right away!
Jake, Windsor, and Slips believe Adam ate his parents, causing them to form a stakeout.
In a satire of the "High School Musical" craze of the time, Jake’s wish to live in a real, live musical comes true after he knocks the wish granting fish, David Coppertrout, out of the Central Stream. He soon realizes that he can't sing and doesn't have rhythm. He wants to take back his wish, but he can't until he gets musically talented.
Mr. Mandrill believes the kids are losing interest in life and decides to exite them with an extreme mountain goat, but Jake goes crazy and starts to think he's a goat.
Adam tries to get his "Special" status at school removed.
Phineas daydreams that he is a knight trying to save Lady Warthog from Jake Spidermonkey.
A human girl raised by possums attends Charles Darwin Middle School.
The students try to act more human when they fear Adam might leave the school.
Adam trains to be a zookeeper over the summer, but he soon discovers that his friends resent those in his profession. Note: This episode was the original series finale.
The night before Thanksgiving, Adam is visited by three ghosts (parodying A Christmas Carol) to help him understand why his friends hate the holiday. At first Adam thinks the animals hate Thanksgiving because people eat turkeys, but it turns out they hate it because of the parades.
Jake keeps trying to pass a note to Adam. Then, Adam gets caught holding Jake's note and takes the blame and Mr. Blowhole writes a letter to Adam Lyon in detention.
Adam and Jake are sentenced to cafeteria duty for accidentally lighting a stick of dynamite.
During class, Adam struggles to find a bathroom to use, but Mr. Hornbill tells him to wait until the bell rings.
Instead of dodgeball class, the students are assigned to dance. As Adam starts to dance, he attracts all the females in the class (who mistake his moves for a mating ritual). Adam attempts to flee unsuccessfully as the girls in class amorously pursue and tackle him.
Dickie Sugarjumper advertises a new trinket called "Pocket Clam." Everyone wants to get one, Adam however thinks they're all worthless.
Bull goes head-to-head against Henry for the title of #1 Grandson, but loses and is given the title of #2 Grandson.
It's the Charles Darwin Middle School's Picture Day and everybody has to be smiling for the camera, because Principal Pixiefrog takes pictures during the hall school day.
When Adam's place at the lunch table is occupied by Bull Sharkowski, he must find himself another place to sit.
Adam and Jake try to stay up all night to pass the test in hibernation class.
Jake and friends try to remake Adam's locker to be banana-themed. But when Adam opens his locker, it turns out to just have a banana in it.
Mr. Hornbill starts to give everybody detention when he doesn't get his cup of swamp-muck coffee.
Mr. Mandrill discovers that the students don't need his guidance. He tries to create problems for them, but only ends up creating a big problem for himself.
It is Animal Punned Poem day and After Adam said the Penguin is mightier than the Swordfish, everyone laughs uproariously with the Penguins while the Swordfish plan to clobber Adam.
