As Madoka and Yurikano wake up and discover they have switched bodies, Muginami ends up taking Yurikano away before an explanation can be made. As Kirius, Izo and Array engage in battle with the Le Garite forces, Lan, Muginami and Yurikano are saved from the crystal anomoly by the arrival of the Vox units, although Midori leaves Yurikano behind after learning it is not really Madoka. As Madoka is forced into an escape pod headed into outer space, Yurikano hijacks a Le Garite Ovid and meets up with Kirius, Izo and Array to fight off Le Garite until Villagiulo and the De Metrio forces arrive. As Lan and Muginami arrive to break up the fight, Madoka inadvertantly activates an emergency broadcast in her pod, in which she broadcasts her deduction that Yurikano is in love with Dizelmine which led her to feel saddened by his fighting with Villagiulo. Just as Madoka is about to drift off into space, Midori manages to rescue her and takes her straight to Dizelmine.

As Madoka approaches Pharos, Midori reacts to her presence and transmits her thoughts to Lan and Muginami, asking Tadoroko to try and get her ban lifted. As the two begin their attack against the enemy, the fleet focuses their attack on Lan whilst Muginami comes up against Villagiulo and a section of the fleet goes to attack Pharos. As Yoko reveals some of her research on the ancient people to Asteria, she manages to convince her to lift Madoka's ban, allowing her to fly up and assist her friends. As the enemy fires at Kamogawa, Kirius, Izo and Array stand to protect it. Just as the girls gain an advantage, Yoko gets critically injured when an enemy Ovid lands in the school, causing Madoka to become stressed which in turn causes the Voxes to once again go out of control and bloom Rinne flowers.

On the day of the cultural festival, Lan and Muginami have to keep a mission given to them a secret from Madoka. Whilst looking around the stalls they helped with, the girls come across Asteria who has Madoka escort her around the festival. As Madoka starts to become depressed at the thought of Lan and Muginami making new friends, she learns from Asteria about the assault Lan and Muginami are making and decides to go after them.

After Madoka knocks some sense into both of them, Dizelmine and Villagiulo agree to work together to resolve the threat to their planets, announcing their unionship at the Intergalactic Conference. The next day, Dizelmine and Villagiulo settle things with Lan and Muginami before setting off. As the Novumundus crew discuss what caused the Voxes to act on their own, Madoka, Lan and Muginami return to the place where Madoka and Lan made their vow to meet again, this time to make a vow not to use their Voxes as weapons ever again. As Yoko demonstrates a new section of the tablet her team are deciphering, Asteria sees a disturbing vision, revealing to Yoko that she herself was responsible for the tragedy that befell Earth 20,000 years ago. .

Asteria Lizamarie de Roschefall, the granddaughter of Novumundos' chairman, comes to question Madoka about the incident that occurred whilst confronting Muginami. As Asteria speaks with Yoko about the Voxs, Lan tells Madoka about the Vox Legend, in which an incident involving Voxes nearly destroyed the world 20,000 years ago. After speaking with Yoko, Asteria decides to ban Madoka from piloting Midori, prompting Lan and Muginami to lock themselves in the hangar as protest. However, Madoka decides to accept the ban, since it wouldn't separate her from Lan and Muginami. Afterwards, Asteria goes to see Villagiulo, refusing to hand over the Vox units.

Madoka, wanting to take revenge against Villagiulio, stands against him in a battle. However, Muginami ends up activating her Vox unit and standing in Madoka's way, telling her that she's only being selfish in trying to take revenge on her behalf. As Madoka argues with her, a mysterious occurrence causes a mysterious flower known as Lagrange to rain from the sky.

Madoka and the others find Dizelmine on the beach, where Yurikano is standing by him. The Rin-ne they are in soon changes as a result of their will changing Dizelmine's heart. As the place soon starts to close up, Madoka insists on taking Yurikano and Dizelmine with her. They soon arrive back in the real world, singing their triumphant Jersey Club anthem which quells the black phenomenom into beautiful flowers which drift off into space. Upon leaving the Rin-ne, Dizelmine ends up as a younger age, much like Asteria did, whilst Yurikano reunites with the KISS members and Moid mysteriously vanishes into thin air. After Madoka graduates from high school, she tells Yoko about what happened ten years ago when Midori saved her from drowning, believing it to be a message from her mother. Meanwhile, the Jersey Club form branches on Le Garite and De Metrio, with Madoka, Lan and Muginami helping out all over the universe.

As Diezelmine and Villagiulo arrive in Kamogawa for the conference, Asteria arranges for them to be trapped in an elevator to have their discussion, which seems revolve around Madoka and the Voxes power. Meanwhile, a Le Garite Ovid crash lands into Kamogawa, its pilot revealed to be the De Metorian princess and Villagiulo's sister, Yurikano, who was rescued by Dizelmine following a war but had lost her memory. Recognising her as the girl she saw in her vision, Madoka tries to see if she knows anything, but to no avail. Wanting to give Madoka a chance to prove herself, Lan manages to sneak her and Muginami aboard Dizelmine's ship back to Le Garite.

As the Jersey Club works on a preparing a cultural festival, Izo becomes inspired by a samurai drama to challenge Madoka to a duel and travels to Kamogawa, prompting Array and Kirius to try and stop him. As Izo is mistaken by some of the other students for Madoka's boyfriend, he is told how Madoka was inspired by Yoko to join the Jersey Club after her mother died trying to save someone. After hearing the story, Izo decides to leave before Madoka arrives.

As Madoka rushes to fight against the enemy Ovid to protect her town, Lan becomes conflicted about a legend Madoka doesn't know of, the fear of which prevents her from being able to pilot her own Vox Lympha. As the enemy, Kirius, tries to ask Madoka to come to her planet, she refuses and the fight resumes. Feeling Madoka is in danger, Lan overcomes her fear and pilots the Lympha, but finds herself up against the other enemy Ovid. As Lan expresses her guilt towards dragging Madoka into this, Madoka lifts her spirits, enabling her to overcome her fears and transform Lympha into its fighter mode, allowing her to come to Madoka's aid, forcing the enemy to retreat. Afterwards, Madoka and Lan decide to name their Vox units Midori and Orca respectively.

As the darkness continues to spread across the earth, Madoka, Lan and Muginami wake up seperated in a strange place similar to where she first met Yurikano. They each come up against a vision of Dizelmine's Vox and fight angrily against it. Meanwhile, Asteria confronts Moid, who reveals he manipulated Dizelmine into opening the Rinne, revealing his motives before receiving a prompt punishment from Yoko. As Madoka sinks into despair over being unable to defeat Dizelmine, she gains encouragement from Midori and is shown a vision of Dizelmine and Villagiulo's past, before managing to find Lan and Muginami. After regaining their resolve, the three resume their battle against Dizelmine, aiming to make him remember the goals he shared with Villagiulo.

Muginami transfers into Madoka's class, which causes worry for the organisation. Later, Youko and one of the organization's representatives talk to Madoka's teacher about her piloting Midori. Youko agrees to let Madoka continue piloting Midori on the condition that she is allowed to continue living at home and attending school. Soon afterwards, Madoka and Muginami participate in an open swimming contest whilst Lan keeps watch on a boat. Spotting her, Muginami decides to play a prank on Lan and tip her into the sea, unaware that she is unable to swim. Realising her mistake, Muginami helps Madoka rescue Lan and performs CPR on her. Afterwards, Madoka invites Muginami to join the Jersey Club, much to Lan's annoyance. Both Muginami and Lan decide to help out at Madoka's family restaurant, with their individual traits attracting many customers.

A man named Villagiulio comes, who Muginami reveals is an ally of sorts. However, Villagiulio soon turns against Muginami for taking the Vox unit for herself, causing Madoka to become angry.

As Madoka becomes conflicted about Muginami's actions, she comes to realise that she hasn't taken Muginami's feelings into account and decides to try and make up with her.