|“||...their new school isn't for superheroes - it's for super villains!||”|
After a mysterious school opens across the street, the students of Super Hero High find themselves up against a new threat. Now, Wonder Woman, Supergirl, Batgirl and the rest of the DC Super Hero Girls not only have to worry about the well-being of their grades, but the safety and security of friends, family and the rest of civilization. The girls must figure out how to put a stop to this evil, new cross-town rival and save the world once again!
Wonder Woman, Supergirl, Batgirl and Green Lantern face off against Cheetah, Poison Ivy, Catwoman and Frost in a school sparring match. The opposing side has the upper hand until Wonder Woman's team strategise by switching partners, earning them the victory. Cheetah doesn't take the defeat lightly, and Coach Wildcat warns her that 'there's no fair in fighting'. As Cheetah's team leave, Wonder Woman, Supergirl, Batgirl and Green Lantern plan on making friendly amends with them after they train to keep their undefeated title. Meanwhile, Lena Luthor, complaining about being a “B list” villain, comes up with another evil scheme that will make her one of the most respected super villains of her time, hiring construction workers to quickly build something 'the size of a school'.
Principal Waller goes on vacation, leaving Vice Principal Grodd in charge. However, Lena Luthor arrives at Super Hero High and masquerades as Waller, taking over the school, releasing her Kryptomites to cause mayhem. Beast Boy convinces Bumblebee and Katana into playing a game of Hyperfly to determine who is the better hero (and also so he could selfishly earn money), but the game lasts for hours and hours. The next day, Professor Oberon teaches a lock-picking class, and as Catwoman is the first one to pick her lock, a Kryptomite quietly throws down a skeleton key, framing Catwoman for cheating. The Kryptomites also frame other students for causing mayhem, such as framing Frost for freezing the water pipes while Grodd and Flash were taking showers, and framing Cheetah for putting itching powder in Wonder Woman's hair before a quick race during P.E. They also frame Poison Ivy for sending Supergirl a package delivery - inside the package is a giant Venus flytrap which attacks Supergirl around the school. Jessica Cruz abandons her driving test, instructed and monitored by Red Tornado, to help defeat the plant. The fight ends up interrupting Bumblebee and Katana's ongoing match, but the plant is eventually defeated, but Ivy gets blamed.
Catwoman, Poison Ivy, Frost, Cheetah and Harley Quinn (who is also sent for purposely causing her own pranks) are lectured by Lena disguised as Waller, who tells them to rethink their positions at the school. Wonder Woman and the Super Hero Girls go to confront Waller and defend Cheetah and the others as their behavior is out of character, as Lena’s holographic disguise malfunctions. Lena dismisses the Super Hero Girls, who decide to go to the villains and tell them they have their support. At Cape and Cowls Cafe, Lena, in the disguise of a hero named "Divide", tells the Cheetah and her crew that the Super Hero Girls are probably to blame for the false allegations and tells the girls about a new school, Uber High. They head off for Uber High, scolding the Super Hero Girls and demanding that they should 'stay out of [their] way'.
Batgirl uncovers that Uber High is backed financially by Lena Luthor, and the group decide to send Green Lantern to infiltrate the new school, while wearing tech gear so the other girls can guide her. Jessica Cruz is accepted by the Cheetah, Harley, Ivy, Catwoman and Frost, and is introduced by the school principal, Principal Taller (who is also Lena in disguise), and the school’s foreign exchange student, Backlash, who Wonder Woman, Supergirl and Batgirl recognize as Lashina. Principal Taller sends the students after a vase inside Project Cadmus, which is, in fact, alien technology. The Super Hero Girls decide they have to warn their friends that their new school is a school for villains. Meanwhile, Katana and Bumblebee are caught by Dr. Fate sleeping through class, having failed a midterm. Fate decides to take the two to the “Globe of Fate” for an extra credit assignment and sends the two off after a mystical necklace, which will "help the school in its hour of greatest need". One of the Kryptomites eavesdrops on this and alerts Lena abour Katana and Bumblebee’s assignment, and she sends the rest of the Kryptomites to the retrieve the necklace first. The now Uber High girls attack Project Cadmus and succeed in breaking into the base, only to be confronted by Wonder Woman, Supergirl and Batgirl. The villains ignore the superheroes' warnings and defeat them brutally before make off with the vase, still with Jessica in tow.
Bumblebee and Katana race towards a temple containing the necklace. The two trigger a trap door and make their way through a booby-trapped passageway, and when they rescue each other from the traps, they show some appreciation for their individual abilities. Wonder Woman tells Jessica to get each of the Uber High students one by one to tell them privately that Lena Luthor is in charge of the school, hoping that they will listen to reason. Lena, still disguised as Principal Taller, sends the villains after the magical stones guarded by the wizard Shazam, falsely telling them that the wizard has turned evil. Green Lantern takes Cheetah aside and tells Cheetah her concerns about Lena Luthor. However, Cheetah reveals that she always had her suspicions about Jessica joining Uber High, and that she is now working with Lena, who appears undisguised. Having set up Lantern and jamming her communication gear, Lena unleashes a gang of yellow fear-inducing Kryptomites against Lantern.
Bumblebee and Katana fight over the necklace at the temple, until Lena's Kryptomites arrive, outnumbering them. Wonder Woman, Supergirl and Batgirl board a bullet train to the Rock of Eternity, and when they arrive at the Wizard’s lair, find that they have walked into Lena and Cheetah's trap and are walled into a chamber along with Green Lantern. They discover that the chamber they are trapped in is magic as the Uber High crew sneak toward the main chamber, where the sleeping wizard Shazam guards the gems they are after. The Wizard goes on a bathroom break, allowing them to remove the gemstones, causing them to be attacked by the stone idols guarding them. They narrowly escape through a portal. Bumblebee and Katana fight off the Kryptomites, but their unrelentless competitiveness results in their loss, causing a rockslide that traps them in the temple. The two reconcile, apologizing for being too competitive, and work together to escape the temple. Unfortunately, as soon as they escape, the Kryptomites have already left along with the necklace.
The Super Hero Girls work together to break free of the temple and are attacked by the angered statues. They are able to escape through Supergirl summoning her psychically controlled Kryptonian jet, which arrives in the nick of time. Back at Uber High, Ivy, Catwoman, and Frost begin missing their friends and Super Hero High, disgusting a now secretly evil Cheetah. Principal Taller sends the group to steal Dr. Fate's Globe, which beings to make them feel uncomfortable about the school. However, Cheetah suggests that they challenge the Super Hero Girls to another sparring match while she and Lena slip in and steals the artifact.
The Super Hero Girls arrive back at school to attempt to tell their teachers what has happened, only to have Coach Wildcat tell them about being challenged to a sparring match by Uber High. Harley, Ivy, Catwoman and Frost face off against Wonder Woman, Supergirl, Batgirl and Green Lantern, but ultimately, the Uber High students realize how much they miss their old school, seeing the fault in their ways and reconciling with the Super Hero Girls. The girls join forces to stop Lena and Cheetah from stealing the Globe of Fate from Dr. Fate.
Lena and Lashina reveal their true selves to the Super Hero Girls, with Lena using the Globe to complete her mechanized super-suit and turns against Cheetah, who reluctantly rejoins her classmates' side. The group attempt to fight Lena, realizing that her mecha suit is giving her the ability to absorb their superpowers. The Super Hero Girls strategise but climbing into their vehicles instead, defeating Lena's mecha. However, the Kryptomites show up with the necklace as Katana and Bumblebee join the battle, and give it to Lena in order to make her powerful. But the necklace actually depowers Lena, returning the Super Hero Girls' superpowers. Lena decides to use her back-up plan, escaping with Lashina and turning Uber High into a giant flying ship, which the group eventually defeats, sending the ship flying off out of control and out of sight.
The Super Hero Girls celebrate their victory as Principal Waller returns from her vacation. Coach Wildcat, realizing that teamwork is superior to working apart, asks if they are all up for another sparring, and the girls agree if they switch up the teams. Beast Boy mischievously plans on making more money from this match, only for Bumbleebee and Katana to menacingly approach him for causing them to argue in the first place, and he makes a narrow escape. Lena's ship lands in a swamp, where she and Lashina decide to start the Legion of Doom.
- In the credits, Poison Ivy is misspelt Poinson Ivy.
- The end of the movie hints towards a possible sequel featuring the Legion of Doom. It is unknown if there were any plans to make a third LEGO DC Super Hero Girls movie, but they were most likely cancelled due to Lauren Faust's TV series reboot.