The story begins with Frankie introducing the events of an eclipse in a faraway land. Inside the mysterious castle of a desert area, a genie named Gigi Grant was being chased by her shadow sister, Whisp, in order to gain her current finder's, Fawn, last wish. While Fawn is unaware of the danger occurring, she is being influenced by the whispers to grant all power to the shadow genie. While Gigi tries hard to keep Fawn aware, the eclipse arrives and Whisp becomes real and gigantic. Seeing Whisp about to use Fawn to take the last wish, Gigi forces herself to break the rules and free Fawn of Whisp’s power using Grimm’s Magic Mirror. Gigi successfully manages to break the spell over Fawn, but shatters the mirror. After the eclipses passes, Whisp returns to being a shadow. Fawn then uses her last wish to pull the mirror, Whisp and Gigi back into the lantern. After a blinding light, Fawn wakes in the middle of the desert as the lantern is taken away to the next finder…
A thousand years later to the present, Monster High welcomes back the students for the new scaremester. Everyone talks about the upcoming events for the year such as the upcoming occultation (eclipse) while expressing what they wished for to happen. One Howleen Wolf, however, plans to take more action as so far as to arrange her name in lights while her shadow friend, Twyla, protests against it. Frankie Stein, Clawdeen Wolf, Lagoona Blue, Draculaura and Ghoulia Yelps spots Howleen and attempts to stop her, however they were too late and are later punished to clean the school attic by Headless Headmistress Bloodgood. Howleen apologizes as they clean while Clawdeen tries to understand her little sister’s reason, but is dismissed by Howleen very quickly. As she moves away and cleans more of the attic, Howleen eventually finds the lantern and releases Gigi. The pink genie introduces herself and explains Howleen is her new finder and therefore is granted thirteen wishes. Howleen uses her first wish to wish the ghouls and herself out of detention. As Gigi grants the wish, they disappear in flash of light and unintentionally frees Whisp. The shadow genie sees the opportunity of another eclipse and follows the ghouls unseen.
The ghouls later arrive at the Maul to fang out as Gigi elaborates of Howleen’s twelve remaining wishes and warns her there is a ‘dark side’ to using them. However seeing Howleen too excited about using her wishes, Clawdeen advises Howleen to take Gigi’s words seriously. Howleen, however, takes it defensively and runs off with the lantern while annoyed of her sister. Later back at Monster High, Draculaura helps Abbey Bominable run against Slo-Mo for Student Disembodied President while Frankie shows Gigi around Monster High. Despite the argument earlier, Howleen took the advise to heart and uses some of her wishes to help her friends: Lagoona turns from ‘Saltwater’ to ‘Freshwater’ for Gil Webber ’s parents to like her, Clawd Wolf along with Heath Burns and Manny Taur get casted on the show ‘Die trying’ and Abbey becomes the new disembodied president. But before Howleen could congratulate herself, Gory Fangtell torments her in the bathroom and leaves her crying alone. Watching from afar, Whisp uses this opportunity to take advantage of Howleen to wish for things more for herself. She summons Gigi, who is alarmed by Whisp and warns Howleen about the wishes. However, Whisp reminds her about the rules and Howleen uses her next wish to become popular.
While enjoying her new wish of popularity, Howleen offers to wish the same for Twyla. Twyla politely turns her down, not comfortable with all he attention. Howleen then leaves her behind and continues being chastised by Cleo De Nile. Frankie then talks with Gigi about her life in the lantern and discovers that she’s lonely and will leave Monster High after the last wish is granted. Not wanting her new friend to leave, Frankie vows to help change Gigi’s life. As the days pass on around Monster High, some of the side-effects of the wishes begin to take effect around the school and causing problems such as Lagoona becoming obsessed with being freshwater, the obstacles of Die Trying become very dangerous and Abbey's ideas as president are not taken well by the school. Twyla then confides to tell Frankie and Gigi that Howleen was beginning to not act like herself and she senses something within the shadows. Frankie asks if Gigi knows anything, but Gigi sadly tells that she cannot say anything due to the Lantern’s magic. Frankie and Twyla then try to find out on their own what was wrong with Howleen, but get dismissed thanks to Whisp's influence. Cleo then appears and irks Howleen enough to wish for Cleo to be turned into a nobody. Clawdeen later sees how Howleen dismisses her friends and finally confronts her of what she was doing. Howleen listens and is about to help after summoning Gigi but is disheartened when she hears Clawdeen doesn’t think she’s mature enough. She then uses her next wish to make Clawdeen disappear into the lantern, leaving her shadow behind and giving Whisp more power.
Frankie, Draculaura and Ghoulia notice the changes and later finds Gigi crying in the garden. Gigi is reluctant to explain (even when learning of the upcoming eclipse) that she is not allowed to influence the finder, but Frankie and Ghoulia points out that they are not the finder and Gigi should be able to tell them. Gigi realizes they are right before leading the ghouls away to the attic to explains everything about Whisp and how Clawdeen got banished to the lantern. She also warns them of Whisp’s plan to use the eclipse and one of Howleen’s wishes to gain all the power to banish everyone and replace them with shadow versions to rule the world. Wanting to save their friends, Frankie and the others help devised a plan to help Clawdeen with the use of an exit to get out of the lantern. They later find Howleen and Shadow Clawdeen in the bathroom and confront her to purposely be wished to the lantern to find Clawdeen, unknowingly leaving their shadow versions behind. Gigi then leaves Howleen alone, alerting her of how many wishes remains.
Inside the lantern, Frankie, Draculaura and Ghoulia successfully find Clawdeen, but not without being confronted by Whisp, who lets them know that she has power within the lantern. Clawdeen then shows the ghouls the ‘Genieology’ telling of Gigi’s story and why she was reluctant to interfere. They use a map to search for the missing shard of the mirror. Meanwhile in Monster High, Twyla is watching from the shadows of any way to help Howleen while reluctantly helping Cleo regain her popularity and Deuce Gorgon’s love. The shadow ghouls then make their move into help Howleen take over the school by replacing Bloodgood with herself as Headmistress and banishing Abbey and Cleo to the lantern, who then join the other ghouls to finding the mirror pieces. The monsters prepare for an eclipse party where Whisp is setting up for Howleen to use her next wish to grant all power to the shadow genie. Twyla follows Howleen and sees that Whisp is the one controlling her. After finding twelve piece, the ghouls find Whisp’s room and realize she has the last piece. After nearly losing the exit orb, Frankie gets it back and returns to Monster High with the other ghouls on magic carpets in time for the eclipse. Whisp tries to influence Howleen to make the wish, but Twyla steals the last mirror shard and assembles the mirror to break the spell. Howleen awakes in time and rejoins her ghouls without making the wish, cause Whisp to fail once again as the eclipse ends.
The ghouls rejoin Howleen, grateful that she is alright. Howleen is grateful her friends never gave up on her as Gigi assures its safe for Howleen to use her last two wishes. Howleen uses the first one to undo all of her previous wishes, much to the delight of Monster High. Gigi is joined by a defeated Whisp, explaining the last wish will send them both back into the lantern. The monsters are reluctant to let Gigi go and plead for her to stay. Gigi expresses she would love to, but cannot as long as she’s bound to the lantern. Howleen then suggests another way as she explains to Whisp she understood her plight before making her last wish for Gigi's freedom and for Whisp to become what she always wanted to be: a real genie. Gigi happily grants the wish, freeing herself and allowing Whisp to become the new genie of the lantern. Whisp leaves with the lantern and falls down into the deep end pool where it will be found again someday.
A party is then held later then night to celebrate the eclipse, featuring a concert performed by Catty Noir . Gil is relieved to have Lagoona back to her real self and not what his parents wanted her to be. Cleo is happy to have Deuce and her popularity back while inviting to share with Howleen and Twyla. Clawd, Manny and Heath almost win on ‘Die Trying’, though have somewhat a traumatic experience. Frankie closes the story with the moral: Everyone has something they wish for, but they might not turn out what you really want.
- Whisp's quest for absolute power and demeanor in the movie is similar to Jafar from Disney's Aladdin (1992) . She also grows during the eclipse in a similar way when Jafar became a genie,
- The objects in the school attic are reference's to the spin-off, Ever After High the item's that appeared are Maddie Hatter's hat, a red apple, a 'drink me' vial and the Evil Queen 's mirror.
- The struggle between Lagoona and Gil's relationship returns as Gil's parents try again to pressure them apart due to bias believes between saltwater and freshwater monsters.
- The photos in Frankie's locker are taken from the events in "Scaris, City of Frights."
- The gag the green goblin being snatched by the tentacle continues.
- The gag of Headless Headmistress Bloodgood's head coming off continues.