The story starts with Frankie narrating about a story about the genie of the lantern Gigi who stops her "shadow" Djinni "Whisp" Grant from influencing Fawn, but the mirror which breaks the influence is broken. The story, after the starting sequence, Frankie meets up with Draculaura, Cleo, Ghoulia, Abbey, Clawdeen and Lagoona and they all discuss wishes for the new year. Outside, Heath, Manny and Clawd attempt to get on the show "Die Trying" but fail.
A while later, Howleen bumps into Gory and is called "fur-gettable". Howleen's best-friend, Twyla, tries to comfort her but she takes it to heart. She hatches a plan to get everyone's attention with a giant Howleen sign, which shorts out leaving Howleen, with Clawdeen and her friends in detention. After a argument about popularity, Howleen unintentionally finds Gigi and gains her 13 wishes. The first she uses to get out of detention. Whisp, having been released alongside Gigi, notices a eclipse in 3 days and sets her sights on prompting Howleen. Both Gigi and Clawdeen tell her to be careful but Howleen accuses Clawdeen of telling her how to use her wishes. Frankie notices Gigi get uncomfortable about the idea of sisters.
In the courtyard, Lagoona and Gil are upset as Gil's parents are preventing them from being together, even in classes. Howleen, not wanting her friend to be upset, uses her 2nd wish to turn Lagoona into a Fresh-Water monster like Gil. She uses her next one to get Clawd, Heath and Manny on Die-Trying and the fourth to help Abbey become Student Disembodied President, much to Cleo's annoyance.
Entering the toilets, Howleen is again teased by Gory and Whisp convinces her to wish to be popular. Gigi tries to convince Whisp otherwise but Howleen can't see Whisp, only Gigi (although Twyla can sense her). She makes the wish and is invited to Operetta's party on the Saturday. Everyone begins to compliment her and invite her to hang out and she is filled with joy.
However, when Headless Headmistress Bloodgood leaves the wishes begin to take their toll, as Die-Trying proves itself to be a tough show to be on, and the role of Student President becomes much busier. Detecting Howleen may be being influenced by the wishes and feeling something dark in the shadows, she asks Gigi about it. Gigi reveals that she cannot tell, as the genie is not allowed to influence what the finder wishes for. Instead Frankie and Twyla go directly to the now popular Howleen, who rejects their help. Howleen begins to feel the strain of popularity, and Cleo confronts her about this. In spite, Howleen wishes for Cleo to be a nobody, which crushes Cleo, as neither her friends or Deuce recognize her.
Howleen's wishes escalate, and when Clawdeen confronts her about this, Howleen wishes for her to disappear, and she is stuck in the lantern, something which causes Howleen to become evil. Clawdeen is replaced by a shadow version of herself. When Clawdeen's friends asks Gigi about it and notify her of the eclipse, Gigi tells them about Whisp, who is influencing Howleen to go against her better nature. When the eclipse covers Monster High, Whisp will become real and if Howleen wishes it, all powerful, able to trap every student in the lantern and replace them with shadow versions of themselves, under Whisp's power. The ghouls go to find Clawdeen, the only other person who can influence Howleen. Gigi gives them an orb which allows them to escape from the lantern, and the ghouls go to find Howleen to send them into the lantern. Howleen wishes so and the ghouls are sent to the lantern, and replaced with shadow versions.
Ghoulia, Draculaura and Frankie end up at the lantern castle, where they are discovered by Whisp. To become popular again Cleo decides to host an eclipse party with Twyla. Inside the lantern's castle the ghouls find a library and rediscover Clawdeen. Clawdeen takes them on a tour of the castle, and find a history of genies. They discover that one of Gigi's previous finders (influenced by the Brothers Grimm) had wished for Gigi to have a sister, which manifested in her shadow, Whisp. Whisp slowly turned the finders against themselves. Knowing this the Grimm's created a mirror to protect the finders from Whisp, which would show them their true selves. The Magic Mirror was shattered during the confrontation with Fawn, and Whisp and Gigi were forced back into the lantern. The ghouls go in search of the mirror shards, which reveals its true self in the shadows. Wherever they finda mirror, Whisp sets a trap, such as blades, water monster pools or lava rooms, which the girls use their combined abilities to overcome.
Howleen wishes for Abbey to lose her presidency, and she finds herself in the lantern too. The shadow ghouls use Scarah's powers of telepathy to find out who likes Howleen, and begins to issue Howleen masks. Operetta, Venus, Robecca and Rochelle confront them about this, and are apprehended. Whisp teases Gigi about her new found friends, but Gigi rebuffs her and tells her there is no friendship from slaves. When Bloodgood calls Howleen into her office, Howleen wishes her fired. Gil and Lagoona's relationship begins to fall apart due to her new fresh water status, and he breaks up with her. Howleen hijacks Cleo's eclipse party, and makes it hers, sending Cleo into the lamp.
The ghouls are unable to find the final mirror room, until discovering the entrance in the shadow of the door. They discover the final piece isn't inside Whisp's room, and plan to escape when the realize Whisp has the final shard herself. A shadow gargoyle takes the orb, and the ghouls go on a high speed magic carpet ride to retrieve it. They succeed and arrive back at Monster High, where the eclipse begins. Traveling through the shadows Twyla secures the final shard, and the ghouls recreate the mirror. Howleen sees her true self in the mirror, and rejects Whisp for Clawdeen. Howleen wishes to undo all her wishes for her twelfth wish and the school returns back to normal. For her final wish Howleen wishes that Whisp could finally live out of the shadows and becomes the genie of the lamp, just as Howleen once was. Naturally, the ghouls celebrate with a magic carpet ride party, although the lantern does end up in the school pool.
- The title "13 Wishes" is a play on the 2010 movie 16 Wishes.
- Lagoona's transformation sequence is loosely designed after the 1486 painting The Birth of Venus.
- When Howleen enters the attic, a purple hat, a magic apple, a ring, and a bottle with purple liquid are on display. These refer to various students and teachers of Ever After High.
- The mirror Howleen drops and breaks is likely the mirror spoken of in the diary of Madeline Hatter from Ever After High.
- As Howleen is walking outside looking for good uses for her wishes, she passes by Rochelle reading a letter and holding a rose petal. These two things are from Garrott du Roque, with whom she reunited in "Scaris: City of Frights".
- The Grimm Brothers are characters from Ever After High.
- Scarah and Invisi Billy are described as an item, which they are shown to become in "Scarah-Voyant". That webisode did not air until two months after "13 Wishes" premiered, but chronologically comes first.
- The first ever in-cartoon mention is made of Clawdia Wolf, who would debut properly in "Frights, Camera, Action!".
- Whisp's motivations and her fragile bond with Gigi are more fully explained in Gigi's 13 Wishes diary, which pays more proper attention to Whisp feeling disposable compared to Gigi.
- There is little consistency in the scope of Howleen's wishes. For instance, her popularity, student disembodied president, and headmistress wishes reduce almost the entire student body into mind-controlled slaves, but "randomly" do not affect various characters. Why the effects of these wishes differ so greatly is not explained. Howleen's wish to undo her previous wishes also has inconsistent effects. For instance, the Howleen masks all disappear on the 12th wish, but none of the 13 Wishes: Haunt the Casbah outfits are changed for 'Signature' outfits, despite them being a direct result of Howleen wishing the girls banished to the lantern. Particularly peculiar is the Die Trying un-wish. Clawd, Manny, and Heath are just pulled from the show, but they have been on it nonetheless, as proven by Spectra's interview and Crash's presence at the party.
- After Gigi and Twyla talk, Howleen called Gigi possible for a wish; thus making her 10th wish, the one related with Abbey being the 11th and the one related with Principal Bloodgood being the 12th. However, by the end Gigi tells Howleen that she have 2 wishes left.
- When Draculaura is doing Abbey's makeup in the washroom, none of her is seen in the mirror. Traditionally, her clothes do show up.
- After telling the story of how Whisp came to be, Clawdeen closes the book. When the screen zooms out, it is somehow open again.
- Throughout the movie, at random parts, both of Howleen's ears are upright.
- Scarah's 3D model is based on her San Diego Comic-Con International 2011 prototype rather than the 2012 exclusive doll. For instance, she has the broader cheeks and the jacket of the prototype. This is a tad curious, considering Wydowna's 3D model, whose history is largely alike but for the fact her doll didn't come out until 2013, is based on her actual doll.
- Gory's 3D model is updated from its backgrounder-ish previous look to resemble her 2D model more.
- As with "Scaris: City of Frights", "13 Wishes" features a lot of fashion. They are: Clawdeen's 'School's Out' outfit, Ghoulia's Scaris: City of Frights outfit with her Skultimate Roller Maze hairdo, all outfits from the Picture Day fashion line, and the entire 13 Wishes and 13 Wishes - Haunt the Casbah lines.
- "13 Wishes" technically has three release dates: It premiered in English in the UK during the weekend of September 21st and 22nd. It became available for download on September 26th on websites like iTunes. The DVD was released on the 8th of October and the movie aired on television on the 25th of that month.
- The DVD of "13 Wishes" contains three webisodes that likely are exclusive to the DVD until some months into 2014: "Department of Monster Vehicles", "Royal Pest Sitter", and "Cookie Creeper". It also contains the Ever After High webisode "The World of Ever After High" as an Ever After High sneak peek.