You play as Reto, the son of two animal researchers who are well-respected by their village (in contrast to Azreth's parents in the previous game). The parents leave one morning to study animals. Reto spots a talking white rabbit who complains about being late and runs off. He leaves the village and encounters the rabbit again, who leads him towards a well (at this point, there are chunks of the world missing for some reason). Reto examines the well and falls in.
Reto ends up in front of a mysterious castle. A succubus gatekeeper approaches and tries to seduce him, only for another succubus, Lewis (daughter of the Queen of Hearts), to come to Reto's aid. After they defeat the succubus together, Lewis says she'll help Reto return to his world. Meanwhile, a masked blue-haired succubus watches from the castle gate.
Later, while going through Stray Coast, Lewis asks Reto about how he came here, and says that the rabbit might be March Hare. They then meet the enigmatic Cheshire Cat, who tells them about Hearts Day: a day when the Queen will drain many other succubi to death in order to increase her own power. When you leave the coast, there's a scene in which Carroll talks with her subordinates, then gives them a mission to retrieve a certain succubus.
While passing through Edible Forest, Reto can fall through a window into a mysterious hut and drink something that shrinks him. He then encounters Alice, another human who ended up in this world.
They arrive at Atuchu Cave, in which three succubus attack Lewis and Reto falls through a pitfall. Reto encounters Carroll, who introduces herself as Lewis' sister and says the other succubi are currently training Lewis, then attacks. She gives Reto a handicap to allow him to "win". She warns Reto that Lewis is merely using him and then leaves. Reto runs back to Lewis and the three succubi leave, but they've drained a lot of Lewis' power.
Reto brings Lewis back to a house in Mel Village and the Hat Merchant gives her medicine to help her recover. Lewis confirms that the three succubi were her mother's minions and thanks Reto for helping her. After Reto leaves, she thinks to herself.
On returning to the cave, Reto can meet Alice again. She explains how her sister yelled at her during a bad mood, causing Alice to walk in the nearby forest, where she met a mysterious white woman who gave her a Joker card, but Alice preferred diamonds so the woman gave her the King of Diamonds instead, Alice put the card in her pocket and was then warped to Wonderland. Alice leaves, and Lewis comments that residents of Wonderland are allocated to suits and numbers, but the King of Diamonds wasn't allocated in the original Wonderland story.
After leaving the cave, there's a scene in which Carroll reports to the Queen of Hearts, who's angry and orders that Lewis be brought back for reeducation.
Reto and Lewis eventually meet the March Hare, but it turns out that she wasn't the one who brought Reto to Wonderland. As they leave the Hare's house, the Hat Merchant (here for a tea party) asks Lewis what she plans on doing about Hearts Day. Lewis says she can't fight her mother and this is why she accompanies Reto, then tries to cover up her slip of the tongue. They leave the house.
In Zendegee Forest, they meet Carroll again. Carroll reveals that Lewis is simply raising up Reto to feed on his power, and is lying about helping him return home. Lewis admits this was her original plan but she now only wants to help him. Carroll attacks but is defeated, she and Lewis argue about what to do with their mother, Lewis claims that they have the same goal, Carroll storms off and says she won't forgive Lewis if she hurts their mother.
Afterwards, they encounter Cheshire Cat again. She says she's betting on whether the two sisters or the Queen of Hearts win, though in confusing terms, and says the sisters will win if they understand the situation.
Later, there's another scene where the Queen angrily asks a subordinate where Carroll is, the subordinate reports that she isn't here and the Queen sentences her to prison for not reporting this earlier. The Queen says that Carroll will be executed as well.
While passing through Papilio Plain (Papilio Hirono in the translation patch), they meet Cheshire Cat again, who still talks in a confusing way. She attacks and, after being defeated, thanks them for the entertainment. She says that the curse can be broken by stirring up the Queen's emotions, but this must be done soon before the Queen's magic increases on Hearts Day, then disappears.
While passing through Proof Undersea Tunnel, Lewis is kidnapped by slimes. Shortly after, Reto is surrounded by slimes but is saved by Carroll. Carroll acts as his new partner and admits that she changed her mind after hearing Lewis' words in their last encounter. They defeat the Slime Queen (who was responsible for the slimes' organized attacks) and rescue Lewis. Carroll says she now wants to work with Lewis to break their mother's curse, and reveals that she's also run away from home.
Finally, the trio return to the castle and confront the Queen of Hearts. The Queen gives Carroll an offer: drain the other two, and her sentence will be reduced to 10 years prison. Carroll pretends to obey, but instead hits the Queen with a spell that harms only the evil. Enraged, the Queen summons her soldiers, but the Hat Merchant and Cheshire Cat appear, the former using a treasure to paralyze all the soldiers. The Queen suddenly groans and, with her original personality, warns her daughters to run. She teleports them away. The Hat Merchant notes how the curse was briefly broken by the Queen feeling strong emotions. The trio confront her again and begin fighting. The Queen has incredible power that makes her seemingly invincible, but Carroll and Lewis appeal to her original self, causing her power to gradually fade. She tries to convince Reto to leave as the succubus sisters will inevitably betray and kill him, offering to spare only him if he agrees, but Reto refuses. Finally, the Queen is defeated and Carroll uses her spell again, breaking the curse.
Back to her original personality, the Queen thanks them and says she'll make amends for everything she's done. Lewis asks the Queen to help Reto return to his world, and the Queen gives him a key that, when used with a magical monument on the castle roof, will open a one-way path back home. The three succubi say goodbye to him, though add flirtatiously that he can always come back to them. Reto uses the key and disappears. The Queen then tells her daughters to prepare balloons as they'll make this a Hearts Day that everyone will remember.
The credits roll, showing the succubi celebrating Hearts Day by releasing balloons. Among other scenes, Alice and Lorina (the latter a talking bird who shows up repeatedly throughout the game; it shares a name with Alice's sister) look at the scenery from a hill, and the Cheshire Cat tells you (the player) that there's more interesting things to come.
Back in the human world, Reto finds that the well has become a simple hole in the ground. His parents approach and, from their reactions, it seems that little time has passed. They go home. Then next day, Reto visits the site of the former well and encounters the White Rabbit again. The White Rabbit says it plans to curse the queen again, that it was responsible for destroying the well, tells Reto to forget about the succubi, and disappears. Afterwards, Reto can go to a well in his village and return to Wonderland from this.
In darkness, a mysterious voice addresses Alice and talks about destroying everything.
Reto reappears next to a suprised Lewis. He explains what just happened and Lewis deduces that the White Rabbit will return to the castle to curse the Queen again. She says Reto doesn't need to risk himself any more, but Reto insists on helping. They hurry back to the castle and confront the White Rabbit in a room. The White Rabbit talks cryptically about the sins against Alice and this story soon coming to an end, then attacks. When defeated, she tells them to enjoy this peace while it lasts, but she'll finish it in the future. She suddenly changes to a different personality, one that doesn't know what's going on. Carroll arrives and explains that the White Rabbit was herself a pawn of someone from a different world, though that someone won't be able to act again for some time as they'll need time to recover their power. The succubus sisters decide to continue investigating this matter.
Once again, there's a mysterious voice in darkness, who mentions Alice and Lorina's names, and talks about revenge and ending the story.
