Several months have passed since Lan and Muginami left Earth. Now in her final year of high school, Madoka spends most of her days thinking about her friends, when Lan suddenly returns to Kamogawa City.

Madoka rushes to try and stop Lan and Muginami from fighting, though has trouble piloting Midori in the process. Just then she hears Lan and Muginami's true thoughts about how they hate having to fight against each other. As Madoka fails to understand why Muginami and Lan must fight as they go into hiding, she once again loses control of Midori. Madoka tries to search for the whereabouts of Lan and Muginami, even going as far as to call Villaguilio. Meanwhile, both Lan and Muginami find themselves drawn towards the Jersey Clubroom, where Madoka eventually finds them. Seeing Lan and Muginami continue to struggle with their feelings, Madoka gets them to kiss and make up; literally. Putting their quarrels behind them, the three decide to reform the Jersey Club together.

As Kamogawa prepares for an intergalactic conference, Asteria calls Madoka, Lan and Muginami about a Vox Particle Control Experiment, the same that Dizelmine attempted on Lan. She explains about how she wants to try to use the power of the Voxes in a peaceful way to put Villagiulo and Dizelmine off their plans. Madoka agrees to undergo the experiment, and although the initial attempts show no reaction from her, Asteria manages to prompt a reaction from Madoka by embarrassing her. However, as they attempt to stop the experiment when Dizelmine and Villagiulo attempt to contact them, Madoka's levels continue to rise, causing a strange red phenomenom to appear in the sky, which starts forming strange creatures. Meanwhile, Madoka is haunted by visions of what appears to be Yurikano, warning her not to open the Rin-ne flower. When Madoka regains her sense, she finds all the creatures had been destroyed and more Rinne flowers have appeared.

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 girls arrive on Le Gartie's ship, Dizelmine explains why he kept Yurikano's presence on the ship a secret from Lan. Later, Dizelmine brings Madoka to where Yurikano is, putting her in an experiment to implant her mind into Yurikano's body. Realising what Dizelmine intends to do, Lan divises a plan to distract the Le Garite troops whilst Muginami goes to rescue Madoka. As Madoka and Yurikano's consciousses meet again, Madoka feels Yurikano shouldn't need to sacrifice herself for other people and decides to fight her to get her to tell Dizelmine and Villagiulo how she truly feels. As the Le Garite ship starts to become covered in a strange red substance, the Vox units launch whilst Yurikano wakes up in Madoka's body.

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. Madoka and Yurikano then return to their original bodies, unbeknownst to Dizelmine, who admits his feelings to Yurikano before her. As the truth is brought to light, Yurikano decides to let go of her feelings so that the universe can be safe, before disappearing into the Rin-ne once again, promising to one day meet with Madoka again.

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. .

As Madoka, Lan and Muginami feel someone is watching them, they are told they will have to move out of their storeroom at the request of the Student Council as the Jersey Club isn't an official club. Deciding they should make the club official so they can keep the storeroom, Madoka recruits a first year student named Reiko Miki, although she turns out to be a bit clumsy. Meanwhile, Yoko meets up with Machiko, who tells her to free herself from the Jersey Club she created in the past. The next day, Madoka learns that Reiko joined the Jersey Club as she wants to pilot a robot like the others. Madoka uses the Tanada Night Festival, in which large Vox balloons are inflated, to explain to Reiko that they are no longer using the Voxes to fight and she should think about what would make her happy. To this end, Reiko decides to quit the Jersey Club in favour of starting up a robot club, although the Jersey Club are allowed to keep the storeroom for a bit longer in the end. Meanwhile, as Asteria ponders the contradictions concerning the 20,000 year old tragedy, Moid steals the stone tablet, converting it into a small shape and presenting it to Dizelmine, revealing to him the memoria imprinted on his body.

Madoka has her hands full as, on top of her usual Jersey Club requests, she has to sort out her post-graduation plans and organise a party for Kirius and Array, who are to leave for their home planet. Meanwhile as Nomundus investigate the whereabouts of Moid, Asteria tells everyone about her involvement in the 20,000 year old tragedy, revealing her real name to be Maycun, a former queen of Le Garite. After a full day of fulfilling requests, Madoka comes down with a fever. As Lan and Muginami look after her, they worry about how to tell her that they intend to return to their home planets once they graduate. As Madoka recovers and joins in the farewell party, Asteria contacts Villagiulo for information on Moid and comes to realise something about him whilst Dizelmine undergoes a Vox Control Particle Experiment under Moid's suggestion. After Kirius and Array take their leave, the Le Garite fleet suddenly appears above Earth and fallen De Metrio ships land upon Kamogawa.

As Le Garite ships open fire against De Metrio's forces, Villagiulo decides to confront Dizelmine personally to find out the reason for his betrayal. Meanwhile, as Madoka, Lan and Muginami decide to take up their Voxes once more to investigate, Hiroshi and Yoko see them off. As Izo, Array and Kirius help keep Dizelmine's guards off of Villagiulo, Dizelmine reveals his craft is a new form of Vox and overpowers Villagiulo, who is saved by the arrival of Madoka and the others. As Madoka tries to get an answer out of Dizelmine, his anger heightens and his Vox changes form, firing off a wave of dark energy across Kamogawa, whilst a circle of Rinne flowers appear around the planet. Dizelmine then proceeds to laugh maniacally and crush Villagiulo's cockpit before opening of the skies, causing a mass of darkness to start covering the Earth.

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.

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.