Negi and the gang go to the Magic World where they encounter Fate.

As Negi and the gang finish up on their training, they prepare for their trip to Wales while enjoying summer vacation.

When a mysterious black rose appears, Negi becomes convinced that his father Nagi is still out there. Upon the urging of the class to let them help him find Nagi, he gives them permission by transforming the class into their Pactio forms.

An intro to Class 3A: Negi arrives at the school and introduces himself as Class 3A's homeroom teacher and gives introductions to the Baka Rangers and Ayaka.

An intro to Class 3A: Negi makes a love potion for Asuna who shoves it down his throat when he tries to give it to her. Negi also introduces Nodoka, Konoka, the Cheerleader Squad, and Asakura.

An intro to Class 3A: Fuuka and Fumika give Negi a tour of the Mahora campus. The rest of the cast is introduced.

Negi tries to makes up to Asuna after saying to her that she shouldn't mind his business.

While training, Yue convinces Nodoka that they cast a spell of the red string of fate on Nodoka. A spell which shows them who her future partner will be. One end connects to Nodoka and the other end connects to Negi.

After defeating Chao, Negi is informed by Ku:Nel that his father is alive in the Magic World. With the door to that world back in Wales, Negi decides to go back home, so Asuna creates a new club to help him search for his father.

The Negima Club heads to the beach to take a break from their magic training but unfortunately for them, a few of their fellow classmates from 3-A have decided to crash their vacation. But they aren't the only uninvited guests in their trip.

Life for class 3-A and company return to normal as they prepare a party for Anya. Yet remnants of a dark power still remain. Anya, Negi, and three Pactio summons put the power away.

Negi, trapped in a magical dimension, is confronted by the controlled Anya. With the assistance of all of his students, he is finally able to save her and allows everyone to escape from the magical wasteland.

Anya, possessing Evangeline through the Star Crystal, turns Asuna against Negi and many of his allies into stone. But with the help of his remaining students, he's able to defeat her by making a Pactio with the vampire, which, alongside Chachamaru, completes his Pactio collection but does not get them out of trouble.

The evil power harassing the group suddenly increases activity just when a valuable tip from Chizuru reveals the mastermind behind the Star Crystals. Lingshen Chao's Armor Card power is revealed, while Eva falls prey to the Star Crystals.

Yue becomes distraught over her feelings towards Negi and how it may affect her friendship with Nodoka. Powerless, Chachamaru and Evangeline remain stranded at their house surrounded by water.

Due to a series of mishaps, Eva becomes gigantic loli. Negi and the gang must endure the attack of the 50-Foot Doll Master.

With almost all of class 3-A in Suka form with child-like behavior, Negi becomes a babysitter. His staff is broken in the process. Nekane advises Negi to have fun and repairs the staff.

Despite her Black Rose baron identity revealed, Nekane continues to live among class 3-A.

Nekane, Negi's sister, is discovered in the Mahora campus bath by Asuna and Konoka. And after much suspicion, by Konoka and Setsuna, it is revealed that the Black Rose Baron is in fact, Nekane. K? invokes her Pactio form...with unexpected results.

An argument between Asuna and Ayaka results in competition in a series of challenges. However, when a Dark Seed magic appears, Ayaka recalls her friendship with Asuna and uses her Armor form to rescue her.

Negi's students divide into three teams in order to live in the ruined Mahora Academy, find out more information about the Star Crystals, and find a way out of the ruined world.

Restoration of Negi's human form is made possible after pactios with the remainder of the class. The group finds a way to escape the Welsh castle only to end up at a ruined Mahora Academy.

While stuck in a Welsh castle, the entire class learns of Negi's secret and a fairy attacks the class. With no other options, the class runs and are split into groups. Meanwhile, Negi is confronted by images of Nekane and Anya.

Negi and his Ministra Magi search for Yue, who tries to avoid them and making a provisional contract. Yue eventually makes the contract with Negi. Many from Negi's homeroom, Motsu and Shichimi, witness the kiss, and Negi is turned into a Chupacabra.

Asuna shifts the focus of the Chupacabra Research Club to find and capture the Black Rose Baron. Haruna and Yue witness Negi using his magic and persuade Nodoka to reveal on Negi's secret. Haruna then makes her provisional contract.

Class President Ayaka is suspicious of certain classmates who are always with Negi and begins to spy on them. Negi and his partners must deal with another enemy and four more possessed students as Kaede and the Twins' contracts are invoked.

During the spring break, Negi and his partners go on a camping trip. Negi demonstrates his magic while a certain ninja trainee makes a contract with him.

To learn more about the Star Crystals and who might be after them, Negi and his partners travel deep into the mysterious Mahora Library Island while Fuuka, Fumika and Kaede also explore the vast book repository. The twins become Negi's newest contracts.

Sayo, Class 3-A's resident ghost is finally noticed by Negi and is befriended by him. Wanting to make more friends in the class, she unintentionally causes havoc among the girls.

Negi and his 3 new partners must face off against Kaede, Yuuna, and Chisame, who are being controlled by the same evil being who has been attacking the school. After initial failure against them, Setsuna gets a provisional contract to release them and Yue becomes suspicious.