The story begins as a mage known as Arcs Sheldart Elbayas has been put on trial in front of a council from the planet "Alphabet". He then escapes through a hole he blew in the building. He flees to a field and is found by the king who is then only a voice. He is sent through a black hole and meets up with Ink as she prays at a shrine. She is surprised that a duck is talking because Arcs was turned into it. He then faints and she takes him home. He awakens in her room and introduces himself. He Tells her she has to become a mage and when she accepts he gives her the "Magi-Mail", which to her is just a regular cellphone. She then goes to Nao-kuns house to help him with his English homework. While there, Arcs finds a dirty magazine on the floor and shows it to Pastel Ink. Nao-kun sees this and kicks her out.

Two mysterious beings, a girl and a tiger like creature(who later transforms into a small cat), appear on Earth and both have the same mission, to get to Arcs. Then Ink gets a distress call and transforms outside of class. Sumi sees this happen. Then Pastel Ink and Arcs get stuck in Dream And Illusion Space also known as "DAIS", an alternate universe created with magic. The cat is revealed to be Kaksu, who was a colleague of Arcs from the Magical Kingdoms.

Sumi, Ink, and company go to Sumi's villa to swim and stay the night. At night, a ghost named Mihoto plays pranks on the girls, scaring them by playing with the lights. Sumi and Ink discover each other's status as a magical girl when they run into Ah-kun and Ka-kun in the bath. They discover a treasure room under the mansion where Dandy saves the girls from a falling wall of spikes with a "Rolling Thunder Kick."

Alice is introduced as an idol. She arranges a visit to see her fans, but never shows up. Sumi and Ink investigate a school where a drunkard is making a ruckus. A giant octopus with panties on its head then attacks the school. Ink and Sumi (who fantasizes of the octopus's potential tentacle attacks) find their magical attacks useless against the creature. Dandy saves Ink once more by throwing a rose at a tentacle. The drunkard from before comes out, has an odd conversation with Ah-kun, and sacrifices himself to destroy the octopus. At night, Alice attacks Ah-kun. Ink appears, but soon after, Alice is forced to retreat anyway.

Alice attacks Ah-kun and Ink again with a giant horse from another time-space continuum. Ah-kun is forced to create a temporal portal to send the giant horse away, but he and Ink get pulled into the same portal by Alice's magical binds. They end up travelling back in time for 10 years. While waiting for Ah-kun to recover his magical energy so that they can return to present, they wander around the neighborhood and run into the 10-year-ago version of Ink's mom, Sumi, and Nao-kun. Little Sumi is scarred for life when Ink tries to teach her English but it's too difficult for her age, while Nao-kun's addiction to video games starts when Ink introduces him to his first video game.

At the school festival, Ink's class is presenting a haunted cafe. Alice uses this chance to test Ah-kun's "true character" by giving him 3 trials. After much ado about nothing, Ah-kun manages to pass all 3 trials with Ink, Sumi, and Ka-kun's help.

The animation staff meet to discuss ways to improve rating, and decide to provide more fanservice for the show. Rina has been acting differently lately such as putting on makeup, and her friends Remi and Ink decide to follow her around to find out why. Finally in a public bathhouse, Rina confesses her reason, and for a minute there it looks as if she has a yuri crush on Remi. But it turns out she was just wearing makeup to cover up an acne.

Ink catches a cold and has to leave school early. Her friends visit her at home. While taking care of her Sumi remembers their friendship from their childhood.

A dangerous enemy named Black Darkness has been unleashed, threatening to destroy the world. Ink, Sumi and their sidekicks travel to the magic kingdom to battle her.

Having completed their mission to save the world, Ink and Sumi return home but they can no longer transform or use magic. Ink becomes depressed because she can't help Nao-kun study English anymore. When Sumi realizes this she devices a plan to help Ink -- by recreating their uniform so that they can cosplay as magical girls.

After putting in a lot of hard work into their studies, Ink and her friends all pass the college entrance exams and enter college. Dandy-san, Alice and others from the magical kingdom all enjoy living in the human world now. When a new enemy appears, Nao-kun's little sister Mio-chan becomes a magical girl to fight her.