- Glassy Prison: Many of the Big Bads of the arcs, after being defeated enough, are put into cubed containers that are decorations.
Year 1
The Leader
A gamma mutant with phenomenal intellectual and mind-control abilities. He takes control of A-Bomb and Red Hulk and threatens to use his gamma cannon to mutate all the other Academy students.
- Amazing Technicolor Population: He's green.
- Big Bad: Of the Gamma Attack event.
- My Brain Is Big: His head is clearly too big for his body, with his oversized brain endowing him with a genius intelelct and telepathic powers.
Ronan the Accuser
A Kree warlord who crashes Knowhere space station into Avengers Academy and proceeds to wreak havoc with his Chitauri minions, with the intent of destroying the students and readying the planet for his master...Thanos.
- Adaptational Villainy: Once again, Ronan is protrayed as a irredemeable villain working for Thanos.
- Amazing Technicolor Population: Like most Kree, he's blue.
- Big Bad: For the Guardians of the Galaxy event.
- In the Hood: A black and green one.
- Marathon Boss: You need to defeat him 7 times in a row, as the most efficient way of unlocking Groot, and then his bonus stages for the materials to upgrade Groot. His attack and health also grows after each stage.
Red Skull
HYDRA Academy's top student, who often breaks into the Academy to try and get others to join HYDRA.
- Hell-Bent for Leather: He wears a leather motorcycle jacket in this incarnation.
- Marathon Boss: For the Civil War event. Defeating him is necessary in order to materials to upgrade several characters up to their final stage and to unlock and upgrade the Winter Soldier.
- Revenge Before Reason: Unlike the more coldly calculating Madame Hydra, who is willing to endure personal setbacks to achieve her aims, Red Skull holds a personal vendetta after losing to Captain America. While Madame Hydra's main aim during Civil War is to pick apart Avengers Academy, learn its secrets and enslave its students for Hydra's aims, Red Skull wants to destroy Steve above all else. His thirst for revenge sees him overthrow Madame Hydra and seize control of HYDRA, only to be defeated by a coalition including Team Iron Man, Team Cap, Crossbones and Madame Hydra.
Cletus Cassidy/Carnage
Another Klyntar symbiote, Carnage is Venom's violent and bloodthirsty second-in-command.
- Axe-Crazy: He just wants to murder everyone in sight. It doesn't help that his host is a serial killer.
- Deep South: Has a hillbilly accent and the newscaster describes him as "southern-fried".
- Dragon Their Feet: Venom takes the lead for most of the event, but after his Heel–Face Turn Carnage takes over for the final stretch.
- Final Boss: Of the Spider-Man event.
- Horror Hunger: Like the other symbiotes, he's always hungry.
- Marathon Boss: Defeat him three times to recruit Venom and seven to trap him in a jail cell.
Wilson Fisk/The Kingpin
- Adipose Rex: Not only is he quite fat, but he also runs his own crime syndicate.
- Age Lift: Instead of being an older businessman, he's a young man with lots of money to spend.
- Batter Up!: He uses baseball bats that break off when he attacks the party.
- Big Bad: Of Hell's Kitchen.
- Deal with the Devil: His alliance with the Hand is this, who in turn seem to be working with Mephisto.
- In-Series Nickname: Loki calls him "King Potato", and it goes viral.
- Once Done, Never Forgotten: He's subjected to memes about him being mashed potatoes that even his own Hand lieutenants rag him on it.
Mephisto
- Big Bad: Of the Halloween arc.
- Deal with the Devil: While his deals give people what they want, it comes with a horrible price.
- Greater-Scope Villain: Of Doctor Strange, as Black Widow discovers he's the one who caused Kaecilius to become evil. He also let himself get captured on purpose and is plotting something with the other captured event villains...
- "Not So Different" Remark: He feels he and Loki should be working together since they're both master liars.
- The Power of Hate: He plans to turn the Academy against itself.
Dweller In Darkness
- Cthulhumanoid
- The Dragon: Not to Kaecillius, but to Dormamu.
- Time Abyss: He has seen the beginning of the world and will be there to see the end of it.
Kaecilius
- Disc-One Final Boss: Of Doctor Strange.
- The Dragon: To Dormammu.
Dormammu
- Big Bad: Of the Doctor Strange arc
- Eldritch Abomination
- Humanoid Abomination: Looks like a man with his head on fire. Nico Minoru lampshades it.Nico: Do you ever think it's weird that there's so many guys walking around with their head on fire?
- I Let You Win: Defeating him in Streak 1 has him declare this is why Dr. Strange and his companions were able to defeat him.Strange: I guess conquering this dimension won't be as easy as you thought...Dormammu: Don't flatter yourself, Doctor Strange. This was nothing more than a test of your powers...Strange: But I like flattering myself...Dormammu: I like making slaves out of anyone who defies me...
- I'll Kill You!: Defeating him the third time has him tell this to Nico.Dormammu: You'll regret this, witch. You and everyone in your family is doomed.Nico: Yeah that's pretty much normal.
Malekith
- Amazing Technicolor Population: Half of him is blue and half of him is purple.
- An Ice Person: He shoots out shards of ice at the party attacking him.
- Big Bad: Of the A-Force arc.
- Endless Winter: He plans to use the Casket of Ancient Winters to plunge the world into an ice age.
- In-Series Nickname: Mannequin
Year 2
Ultron
- Big Bad: Of the Ultron arc.
- Kill All Humans: He plans to eradicate every last human on earth.
- Red and Black and Evil All Over
Robo-Cap
- Dumb Muscle: It doesn't seem to have much of a real personality other than repeating lines the real Captain America has said and other statements that almost seem like a parody of how Tony/Ultron thinks Steve would act. This makes it seemingly the dumbest and least advanced AI-wise of Ultron's minions.
- Evil Knockoff: A robot clone of Captain America.
Jocasta
- Defector from Decadence: Due to the below, she turns on Ultron the moment Viv Vision frees her from his control, becoming a recruitable hero.
- Perky Female Minion: She was created using Wasp's brainwaves after all.
- What The Hell, Villain?: She calls Ultron out when he starts treating his robot soldiers as expendable, pointing out he'd claimed he was rebelling against humanity for robots' sake.
The Destroyer
- Brain Uploading: Ultron uploads Wonder Man's personality into the Destroyer to make it at least vocal.
- Final Boss: Of the Ultron arc.
- Living Weapon: It was stolen by Ultron during the A-Force event while nobody was looking.
Kang the Conqueror
- Big Bad: Of the Young Avengers arc
Fin Fang Foom
- Attack of the 50-Foot Whatever
- Big Bad: Of the Monsters Unleashed arc
