A year after the events of Kirara, Kuromi and Baku are imprisoned in a dungeon in Mari Land. They make their escape with the Melody Key and the Melody Bow, but in their haste forget the instruction manuals. They flee to the human world, and shortly after arriving, Kuromi discovers the power of the Melody Key, which makes wishes come true using the power of darkness. If the person who wishes enjoys the nightmare, he or she will produce Black Notes, which Baku promptly eats to store them. What neither one of them realize is that when 100 Black Notes are gathered, the Spirit of Dark Power will be revived to destroy the human world and devour all the humans' dreams. Because Mari Land is formed from the dreams of humans, even the incompetent king is able to sense danger to his people. He gives the Melody Takt to My Melody and sends her to the human world, with a mission to collect 100 Pink Notes to create the Dream Power to combat the Spirit of Dark Power. Along the way, My Melody meets a human girl named Uta Yumeno, and her world is about to change forever.
Set a year after Onegai My Melody, the story revolves around Kuromi and Baku's second escape to the human world as they this time obtained a new Melody Key and the Melody Pick, an item associated with the Spirit of Dark Power. Because of this, the King of Mari Land appointed My Melody once again to capture both fugitives and prevent the Spirit of Dark Power from resurrecting for the second time. In the human world, Uta misses My Melody and wonders what she is doing right now back at Mari Land. But then a new student named Jun Hiiragi arrived from England at Uta's school, and she notices he was Keiichi's little brother. Baku and Kuromi also arrived in the human world and learned that if they collected 8 black notes (do, re, mi, fa, sol, la, si, high do) that coincide with the Solfège scale, their wishes will come true and decided to wreak havoc in the city once more. Back at Mari Land, Keiichi Hiiragi is being judged guilty of his crimes against Mari Land, and to make up for it, he must help Uta and My Melody fight the darkness, but in secret, or he'll be severely punished. It's up to Uta and Melody to stop the Revival of the Spirit of Dark Power once again before it's too late.
A year after the second defeat of the Spirit of Dark Power, My Melody and her friends went back to Mari Land until Baku "dropped a bomb" in the middle of the flower field, taking out black notes all over Mari Land and the human world. After a short while, Mari Land had their "high court" and took the king off the throne. When the time came to choose the next ruler, a black note came to the minister, turning him into a "Huff-Huff" which is a residue of Dar-chan. My Melody refreshed him and was chosen to be a candidate for princess. However, she has to pass a trial by turning all of the black notes into Twinkle Gems to put in her crown. As soon as Kuromi heard this, she was outraged as she wanted to become the princess as well, but then a very mysterious woman came with an intriguing offer. Kuromi now has to collect Anger Gems and put them in her crown to become the Dark Princess and rule over Mari Land. The two decide to go to the human world and collect every black note for them to become the next ruler of Mari Land. Unbeknownst to everyone, the spirit again will make its rise as he intends to plunge both Earth and Mari Land into eternal darkness.
Set before the events of the Uta Arc, Mari Land is celebrating a special event that involves watching the Shooting Star, on which they can grant someone's wish. In the human world, Kirara Hoshizuki, a normal elementary girl, is watching the stars that night until she is visited by the king of Mari Land, who invites her to his world. As the king takes her to Mari Land, she meets My Mel…

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The music for all four seasons of the anime was composed by Cher Watanabe, whose other notable works include the soundtracks of Kinnikuman Nisei, The Prince of Tennis, Sensual Phrase, Idol Time PriPara, Maken-ki! and Jewelpet Kira☆Deco!.

Opening Theme
• Oto Melody (オトメロディー, Otomerodī)
Ending Theme
• My Dream! My Melody (マイドリーム!マイメロディ, Maidorīmu! Maimerodi) (EPS 1-28)
• Power of Dreams (夢見るチカラ, Yumemiru Chikara) (EPS 29-52)
Opening Theme
• Love♥is Coming (コイ♥クル, Koi ♥ Kuru)
Ending Theme
• Hare☆Sora (ハレ☆ソラ, Hare ☆ Sora) (EPS 1-27)
• kuru kuru kuru (EP 28)
• I Am Rabbit Ear Mask (おれはウサミミ仮面, Ore wa usamimi kamen) (EP 29) (special ending)
• Dream! Dream! Dream! (ドリーム!ドリーム!ドリーム!, Dorīmu! Dorīmu! Dorīmu!) (EP 30)
• Romi's Dream (ロミーの夢, Romī no yume) (EP 31) (Special ending)
• Let's Hold Hands (手をつなごう, Tewotsunagō) (EPS 32-52)
Opening Theme
• Kirikirisuu (キリキリスー, Kirikirisū) (EPS 1-27)
• Chu☆Please My Melody (Chu☆おねがいマイメロディ, Chu☆Onegai mai merodi) (EPS 28-52)
Ending Theme
• Cheek Chu♡Chu♡ (ほっぺにChu♡Chu♡, Hoppeni Chu♡Chu♡) (EPS 1-27)
• Power of Dreams (夢見るチカラ, Yumemiru Chikara) (EPS-29-52)
Opening Theme
• Glitter Sparkle★彡 (きらきらキララ★彡, Kira Kira Kirara ★彡)
Ending Theme
• Jumping to the Starry Skies (星空ハヤトチリ, Hoshizora hayatochiri) (EPS 1-27)
• Space (Star) Flamenco (宇宙(ほし)のフラメンコ, Uchū (hoshi) no furamenko) (EPS 28-51)
• Let's Hold Hands (手をつなごう, Tewotsunagō) (EP 52)