Sasami meets a new girl named MIsao and becomes her friend. When Misao takes Ryo-Ohki from the new school nurse, Washu, the girls get lost underground, where they learn of each other's magic.

Misao and Sasami learn about their heritage, with a new person joining them in the Magical Girls Club: Makato. However, she learns the hard way to be careful about her decisions.

A marathon is held at the school to celebrate the long-awaited return of Tsukasa, a popular student, to the campus. When she vanishes not long afterward, Sasami travels to the house of Tsukasa to find out the reason for her disappearance.

Anri realizes that anything she writes in the magic notebook she has, appears in real life. However, since she has only been writing colorful insults as of late, these hang overtop Sasami and her friends.

Sasami realizes she needs permission from a parent so she can go on a field trip to the World of the Witches, but her father refuses to give permission. She hopes that he will change his mind before the train leaves the station.

The adventure in the World of Witches continues, with Sasami meeting a boy named Amitav who seems to know about her. The loneliness of Misao fades away when she meets other lonely girls in this world!

After Sasami thinks about Amitav after completing a school assignment, she and Misao travel to the World of the Witches again. However, a friend has to save them when they get lost.

Miso, while at the Niko-Niko Bazaar, she realizes she is working with Kozue and Chiaki. While it is a good way to know the friends of Sasami, Misao keeps messing up again and again!

The job of Ms. Washu is challenged after Mr. Tonobe does an investigation of the Cooking Club. Sasami and the girls come to the rescue, hoping to save her with their culinary skills.

While Asami wants to be an apprentice for the Magical Girls Club, and when Sasami and the other members of the group learn why, they attempt to reunite Asami with her deceased parents.

Sasami and her friends are invited to be part of the Magical Girls Tournament. Their excitement for this wanes and fades when the grueling sessions ordered by Ms. Washu test their friendship.

Misao becomes torn between her loyalty to the Magical Girls Club and Monta, with her emotional issues possibly causing her friends to be unable to attend the Magical Girls Tournament!

While the team of Sasami is behind, they have one event remaining, struggling to cover, with magic, the bare branches of a tree with blossoms of happiness and love, the father of Sasami gives Ms. Washu news which startles her.

Having impressed the judges at the Magical Girl Tournament, the Magical Girls Club is invited to a special Magical Girls summer camp in the World of the Witches.

Sasami feels weird about some the skills the Magical Girls are learning at the camp, as does Ms. Washu, who sees the potential to either right past wrongs or do the opposite.

The storytellers have a short window of time to protect the Magical Girls from the power of the Great Cauldron, especially when the Chief Sorceress is requesting that Sasami and her friends reach into the deepest, darkest parts of their souls.

When Ms. Washu bans the Magical Girls from going back to the World of the Witches, Misao becomes upset. Little do they know, but the World of Witches will come to them in a way they cannot expect.

Itoki is out for Washu, and when the Magical Girls join the skirmish, Misao and Sasami discover a new power, with some people they know taking notice of this development.

Misao tries to do something for Monta, but the reaction from him sends her down a path that leads to a place which is far removed from the Magical Girls Club itself.

Misao, after hiding in the World of Witches, gains a position of honor due to her growing magic skills, and even a new title.

The friends of Misao venture into the Tower of Twilight to save her, but the question remains: who will save Misao's friends?

The Chief Sorcess tells Misao to try to access the deepest parts of her soul. While this may not happen, a meeting with a person she is familiar with may give Misao all the negativity she needs.

The World of Witches' dark magic has changed the attitude and appearance of Misao, resulting in a dangerous rescue attempt by Sasami.

While the Chief Sorcess wants some of Sasami's power, the Magical Girls understand that the magic of friendship itself can effectively battle evil. As such, they realize that they can trust each other and work as one, then humanity can be saved.

Even though normality seems that it is returning, Itoki tells them of a new magic trouble, with Ginji realizing that he can only stop this by hurting those closest to him.

The Magical Girls realize they must depend on one another to fight their foes from the World of the Witches, as they know that only true friendship between them can save the world from calamity.