A young high-school girl, Ruko, receives a deck of cards, the WIXOSS. In the deck, she finds an unusual talking card. Bewildered, she meets Yuzuki, who she calls herself a "Selector." Soon, Ruko finds herself in battle to be the "Eternal Girl."

Ruko, along with her new friend, Yuzuki, come across a battle of Selectors, Akira versus Hitoe. Yuzuki must now prepare to fight the winner, Akira.

Ruko finds herself in battle against Hitoe, and taps into a desire she has never felt before. Meanwhile, Yuzuki's battle ensues against Akira.

Ruko and Yuzuki become friends with Hitoe, with hope for a lasting friendship. Akira, wanting to battle Ruko, faces her, but then Iona appears...

While waiting for Ruko and Yuzuki, Hitoe is defeated in battle. The repercussions from Hitoe's third loss is beyond Ruko and Yuzuki's imagination...

Ruko battles Akira with a resolve unlike before. Meanwhile, Yuzuki comes to a resolve on her own after a meeting with a new Selector.

As Ruko seeks answers, she comes in contact with Iona who soon senses affinity towards Ruko. Later, Ruko and Yuzuki is contacted by Akira...

After Yuzuki parts ways with Ruko, Yuzuki wins to become an Eternal Girl, but... Later, Hitoe gets a new deck of WIXOSS and finds a new LRIG...

Word spreads of the intimate, yet forbidden love Yuzuki has towards Kazuki. Meanwhile, Ruko learns the horror of what happened to the 'true' Yuzuki.

The mysteries around WIXOSS begin to reveal, with an unusual girl at center, Mayu. Meanwhile, a message is sent from Iona to the Selectors...

New secrets unravel with the mysterious girl, Mayu. Iona gathers the Selectors to have battles, with an ulterior motive in Iona's mind...

Ruko's battle finally comes to a close. Everyone has made a choice to their ways, and the results are...

Following the incident, Ruko has been trying to have fun spend time with Hitoe and Yuzuki, but is still troubled by her memories of Tama. Stumbling across a WIXOSS tournament in a market, they are approached by Chiyori, who challenges them to a battle. They refuse and try to explain the true nature of WIXOSS to Chiyori, showing her what happened to Yuzuki, but Chiyori remains deluded by her fantasies. Meanwhile, Ruko continues to be troubled by Iona, whose wish was to become her LRIG, realising that, despite refusing to battle, she can't bring herself to throw her away.

It is revealed that Akira, who had become a recluse ever since receiving her scar, was approached by Ulith, now possessing Iona's body, who stated her admiration for her. Using Iona's position, Ulith helps Akira get her career back on track, though eventually asks for something in exchange. Later, as Hitoe and Yuzuki learn that Akira is seeking out Selectors, Akira appears before Ruko and Iona, challenging them to a battle with her new LRIG, Milulun. With Ruko becoming overwhelmed by Akira, narrowly avoiding defeat when their match is interrupted by a security guard, she laments that she isn't able to have fun in battles without Tama and her friends with her. Meanwhile, Chiyori is approached by Ulith.

Ruko briefly runs into Hanayo, who tells her to keep on battling, while Iona continues to try swaying her into taking advantage of her for the sake of battling. Feeling that she only enjoyed battles when she was with Tama, Ruko tries Iona for information on Tama's whereabouts, only learning Mayu's name. Meanwhile, in another world, Tama desires to see Ruko again despite warnings from Mayu, who she seems to remember from somewhere. Later, Ruko learns from Yuzuki and Hitoe that Akira is spreading rumors about WIXOSS to bring out more Selectors, eventually confessing that she had fought against her. After scolding Ruko for acting on her own, Yuzuki and Hitoe state that they wouldn't be happy if she was to disappear, even if it were for their sake, and agree to help her with her search for Tama. Later, Ruko and the others come across Chiyori being challenged by Ulith, who now wields Tama as her LRIG.

As Tama reluctantly follows Ulith's commands to fight against Chiyori, Ruko senses that Tama isn't having fun with battling and apologises for not sharing her true feelings with her before. After defeating Chiyori, Ulith tells Ruko to battle her if she wants Tama back, though Tama urges her not to do so. Later, the girls hear Chiyori mention a White Garden, which Yuzuki remembers as the room she ended up in upon becoming a LRIG, and ask to borrow her WIXOSS novel, which seems to be closely tied to the secret of the LRIGs. Determined to find the truth, the girls try to get in contact with the book's author, Futase Fumio, who they believe may be a Selector with knowledge about Mayu. Later, as Ulith prepares to make further use of Akira, Ruko and the others are called by Futase to meet up with her.

Futase explains she is fully aware of WIXOSS' secrets, but still desires to battle, agreeing to tell what she knows if someone beats her in a battle. With Chiyori already having two losses, Ruko steps in to battle against Futase and her LRIG, An. With Ruko struggling to bring out her full potential, Iona tells her that she needs to get serious if she has any hope of saving Tama. With this new determination, Ruko manages to grow Iona into a previously impossible Level 5 LRIG and win the battle. Futase then reveals that she herself was a LRIG whose Selector was the real Fumio, who initially wanted to achieve her wish by her own esteem. She eventually gave into battles and soon became an Eternal Girl while Futase took Fumio's place, during which she overheard Mayu mention about a "Girl of Black" and a "Girl of White", which Fumio believes that "Girl of Black" was referring to Iona.

Futase further reveals she feels burdened by Fumio's wish, as she needs to keep writing consistently to keep it fulfilled, becoming a Selector so that she could once again meet Mayu and find more material to write about. As Ruko becomes more determined to free all LRIGs so that they won't have to suffer as Eternal Girls, she discovers Iona has suddenly come down with a fever and tries to do what she can to help her. Later that night, after Hitoe leaves Yuzuki with Ruko that night, she is confronted by Akira who, upon finding that she is unable to battle without Yuzuki with her, takes her hostage in order to lure Ruko and Iona out. When Ruko arrives to confront Akira, she discovers her true opponent is actually Ulith.

Ulith punishes Akira for her unsightly tactics, expressing her joy of breaking things and people and stating her wish is to have everyone continuously suffer in the LRIG cycle. Fearing for Hitoe's safety, Ruko agrees to battle against Ulith in order to rescue her. As Ruko and Tama battle against each other seriously, Tama urges Ruko to defeat her quickly using Iona's Level 5 form, with Tama barely withstanding Iona's attack. It is then that Iona recalls that Mayu is actually the mother who gave birth to both Iona, the Girl of Darkness, and Tama, the Girl of Light, at which point Mayu deals her own punishment to Iona.

Iona explains that Mayu was once a girl who grew up in a secluded room, unaware of the world outside until reading a book about friends. Finding a WIXOSS deck and needing someone to play with, Mayu created Tama and Iona, originally named Shiro and Kuro, as imaginary friends who would play the game together, eventually coming up with the sadistic rules of the Selector battles that would soon become reality. Iona further explains Mayu's wish is to have revenge on those who live in the outside world, while her own fate was to repeat the cycle between Selector and LRIG, which was changed after meeting Ruko. Tama also says how she at first forgot Mayu, but now remembers. As Iona and Tama seek to become friends with Mayu and free all the LRIGs, Ulith infects Tama with her darkness, growing her into a dark Level 5 and forcing her to beat Iona with her own hands and win the match. Akira, driven insane by Ulith's betrayal, stabs her with a fountain pen, leaving her bleeding as she seeks her next target.

As Akira seeks out more battles in order to heal the scar she inflicted upon Ulith, Yuzuki theorises Mayu's true wish in creating the Selector battles was not necessarily revenge, but to show others how lonely she was. Later, when Chiyori comes around asking for a battle, Hitoe agrees to battle against her, feeling that she may be better off if her wish to be part of the WIXOSS world is reversed. During the battle, Eldora reveals she was thinking the same thing and had been planning to lose in order to spare Chiyori from the pain of battles. Despite Chiyori's objections, she is unable to draw the cards needed to turn things around. Meanwhile, Ulith, who had been treated for her injuries, is confronted by Akira.

Following her battle, Chiyori loses her memories surrounding WIXOSS while Eldora, certain she'll be able to become friends with Ruko and Hitoe some day, takes her leave. Meanwhile, Akira states her desire to repeat a cycle of LRIG and human in order to keep scarring and healing Ulith and battles against her, but is again beaten by Dark Tama. After receiving some anonymous directions from Hanayo, Ruko and the others find Iona's body, finding it to be inhabited by the original Iona Urazoe. The real Iona explains how she became a LRIG as a result of a wish not to be herself anymore, her desire to remain as she was coming as a surprise to Mayu. After Iona explains how she returned to her body when she felt it become hollow, the others come to the conclusion that Ulith made her wish come true, albeit with Tama refusing to take over Iona's body, as she didn't want to become human at the expense of others. After seeing the original Iona off, Ruko states her plan to become an LRIG so that she can find Maya and Tama, giving Iona the new name of Yuki. As Mayu locks Tama away, Ruko and the others decide to confront Hanayo.

Hanayo explains that even though she herself has fallen in love with Kazuki, she doesn't want to betray Yuzuki. Kazuki overhears this and learns the truth, leading Hanayo to try and run off, only to suddenly collapse in the process and become hospitalized. As Yuzuki worries that Hanayo will disappear if she can't fulfil her wish, Yuki believes she can and Ruko might be able to reach Tama during a battle against Hitoe and Yuzuki. Sure enough, Yuki manages to get in contact with Tama, encouraging her to grant Ruko's wish alongside her. Together, they make Ruko an Eternal Girl, showing Hitoe and Yuzuki a glimpse of the white windowed room, where Kazuki theorises they may find the real-life Mayu. Ruko and Yuki arrive at the white windowed room to try and talk things out with Mayu, but Ulith also appears, declaring Mayu as her Selector and challenging them to a battle. As the two pairs battle, Yuki starts disappearing as a result of Iona returning to her original body, so Ruko takes her and goes off in search for Tama. Both Ruko and Hitoe's group then learn that the real Mayu is already dead, before Mayu attacks Yuki with a Level 5 attack.

Tama manages to escape her imprisonment and rejoins with Ruko, who combines Tama and Yuki into one LRIG, who is also named Mayu after her true feelings, resuming their match against Mayu and Ulith. Meanwhile, Hitoe and Kazuki enter Mayu's room in the real world, commenting on what a lonely place it is. Mayu laments how she was never given the opportunity to 'select' before she died. Returning to Mayu's not-quite-real room, Mayu gives Ruko one opportunity to guess what color card she chose in order to win the game. Ruko correctly guesses that the card Mayu chose was non-colored, resulting in Ulith being destroyed. Afterwards, Ruko embraces Mayu, allowing her to pass on into the open world. Ruko then changes her wish slightly so that all LRIGS, including those who were LRIGs to begin with, would become girls, completing her contract with the new Mayu. With the Selector battles over, with all girls returned to their original forms, Ruko awaits the day when she can finally meet Tama as a human. It ends with Tama, shown to be a human now, sitting on a rooftop.