In the near-future, the world's energy problems have been solved thanks to a scientific power known as the Manifestation Engine which provides energy from the sky. On the island of Izu Oshima, Akane Isshiki is living a simple life with her sister, Momo, and her grandfather and creator of the engine, Kenjirou. As Akane eagerly awaits the arrival of her classmate, Aoi Futaba, who is travelling to the nearby Blue Island for treatment, she and Momo hear an explosion coming from their home and discover that Kenjirou has somehow switched bodies with an inanimate ferret doll as the result of an experiment. Undeterred by his new form, Kenjirou gives Akane his latest invention, a strange key, in order for her to fight against a strange alien mech, known as an Alone, that is attacking Blue Island, where the Manifestation Engine is stored. As Aoi's transport is hit and crash lands on a ledge, Akane and Kenjirou rush to their location, but Akane is soon struck by her fear of heights that she gained during a traumatic incident. When Aoi starts to fall towards the sea, Akane overcomes her fear and dives after her which activates her key, giving her a special suit known as the Vivid System which stops Akane and Aoi from falling. Kenjirou explains that this system is for Akane and Aoi to fight against the Alone.

As Kenjirou instructs Akane and Aoi to undergo 'docking', Aoi receives her own Ignition Key, allowing her to also transform using the Vivid System. Receiving weapons to go along with their new abilities, Akane and Aoi begin fighting against the Alone whilst protecting the innocent. Meanwhile, Kenjirou contacts the head of the Manifestation Engine's management bereau, Yuuri Shijō, in order to gain military support in assisting the girls in fighting the Alone. After knocking out the Alone's core, stopping its movement, Akane and Aoi attempt the Docking Operation, but it fails due to one of them subconsciously rejecting the fusion. As Aoi worries that she might be the one causing it to fail, she thinks back to when she first became friends with Akane, who gave her a tomato on their first meeting. Meanwhile, a mysterious girl fires a glowing arrow into the Alone, bringing it back to life and changing it into a more powerful form. As the girls find their attacks ineffective against the Alone's new form, Aoi confesses to Akane that she actually hates tomatoes, the reason the docking failed being that she didn't want her to find out when their memories combined. Akane tells her that she already knew about that, but admired her perseverence to eat them regardless and assures her they are best friends. Reconfirming their friendship, Akane and Aoi perform the Docking Operation, fusing together to become Vivid Blue and combining their strenths to destroy the Alone. The next day, as Akane, Aoi and Momo discover their school has been obliterated as a result of the battle, Mizuha Amagi, an officer for the National Defense Force, informs them they are being transferred to a new school.

As Akane, Aoi and Momo begin their first day to New Oshima Academy, Akane, who was using the Vivid System as she was running late, ends up meeting kendo club member Wakaba Saegusa, who becomes shocked when she counters her attack. After Akane and Aoi officially transfer into Wakaba's class, Wakaba chases after Akane demanding a rematch until she ends up bumping into Momo, deciding to take her to the nurse's office. As Wakaba and Momo get acquainted, Akane overhears how Wakaba wanted a rematch to prove she's the strongest. After her dad tells her to think about what 'true strength' is, Wakaba formally challenges Akane to a serious kendo match, which reminds Wakaba of how fun kendo used to be for her. Just then, their match is interrupted by the appearance of a serpent-like Alone. As Wakaba comes to realise what true strength is from watching Akane and Aoi fight, she asks to fight alongside them, granting her her own ignition key. As the mysterious girl powers up the Alone again, Akane and Wakaba dock to become Vivid Green and defeat the Alone.

Akane, Aoi and Wakaba's latest fight against the Alone are observed by Himawari Shinomiya, a girl who spends her days confined to her room and participates in classes through a camera. Following the battle, Wakaba starts training Akane and Aoi so they can safely dock in battle. As the girls attend gym class, Himawari spots Kenjirou through her robot's camera as he investigates who's been hacking access to files on the Alone, before it is smashed by a wayward baseball hit by Akane. The girls go to Himawari's apartment to apologise, where Himawari asks to inspect Kenjirou, which Akane passes off as a stuffed toy named Uso. Noticing Himawari has a thing for factories, the girls dress her up and take her to see one of them. Just then, the factory they are visiting is attacked by the Alone from the previous day, which had undergone an evolution. As the girls transform to defeat it, Himawari heads to the plant to shut it down, but soon gets caught up in a cave-in. Recalling how she was betrayed by her previous friend, which led to her to become a shut-in, Himawari is rescued by Akane, who kept her promise to come back for her. Touched by this, Himawari gains an ignition key, joining the girls in their fight. After the Rei powers up the alone again, Akane docks with Himawari to become Vivid Yellow and defeat the Alone. Following the battle, Himawari decides to start attending classes before asking Kenjirou for his autograph.

Akane tries to get to know her quiet classmate, Rei Kuroki, unaware that she is the one assisting the Alone. As Akane decides to follow Rei after school, she sees her save a child from a falling piece of construction. As Rei returns home, she is visited by a crow, who punishes her for saving the child via a mark on her neck, reminding her of her mission. That night, Rei goes on a mission to destroy the Manifestation Engine by herself, but is forced to abort when she is discovered by security robots. The next morning, Akane finds her washed up on the shore and takes her back to her place to help her recover. As Rei panics when she realises she has dropped a key precious to her, Akane is called into action as an Alone appears. Meanwhile Rei, who was promised by the crow that she would able restore the world she came from and bring back her parents if she assisted the Alone, prepares to fire another arrow, but falls unconscious before she can. Returned to Akane's place again, Rei feels relieved when she is reunited with her key, which Akane and her friends helped search for, although she declines Akane's offer of being friends. Afterwards, Akane goes to the hospital to visit her mother, Mashiro, who assures her that Rei will open up to her someday.

Whilst Akane's class goes on a summer school field trip to Shikine Island, they are requested by Mizuha to turn in their Operation Keys for the duration of the trip. Unbeknownst to the girls, this is part of an experiment by Kenjirou to increase their 'friendship power'. To this end, he 'kidnaps' Rei and puts on a phony Alone alert, leading the girls towards an obstacle course of his design, filled with all sorts of traps. Not considered in his plan, however, was Rei escaping from her hold and assisting the girls in a not-so-subtle disguise. Not wanting to be deterred, Kenjirou brings out a large mech to confront the girls, but it is defeated thanks to the combined efforts of Akane and Rei. Afterwards, Momo gets Kenjirou to apologise for his deceit whilst the others thank Rei for her help.

As Akane struggles with her studies due to a lack of sleep, Mizuha tells her that she'll need to do well on her next test or otherwise give up her part-time job. Upon deciding to help her out with a study session, Aoi, Wakaba and Himawari try to get Rei to join them, but she keeps refusing. Later that night, after receiving another harsh reminder of her objective from the crow, Rei learns about Akane's link with the Manifestation Engine's inventor. Learning this, Rei decides to accompany the others on their study session with Akane. Whilst investigating her home to find something of use, Rei comes across the fridge where Kenjirou's body is being preserved, though the gang are quick to cover this up. As Rei learns to grow accustomed to the others, she takes her leave when she is reminded of a certain wish. Just then, an electro-magnetic Alone appears, shorting out every electrical device it passes by. Akane manages to destroy most of it with Vivid Yellow, but a fragment is hit by one of Rei's arrows, causing it to change its form and launch an attack at Akane, shorting out her Pallet Suit and sending her pummeling.

Akane is taken into intensive care whilst the Alone that attacked her wraps itself into a cocoon on the Tokyo Skytree. Despite their wishes to stay by Akane's side, Aoi and the others are sent home to rest up. Discovering Akane's Naked Rang which hadn't disappeared when she lost her transformation, Aoi believes that Akane is still fighting. Whilst discussing how to fight against the Alone, they find their options limited since the girls are unable to dock without Akane, forcing the military to consider more drastic means. Later, Aoi runs into Rei, who tells her how forgiving Akane is to others. Strengthening their resolve to help Akane as much as they can, Aoi and the others decide to fight against the Alone, taking Akane's Naked Rang with them. Their plan to stop it before hatches is thwarted after Rei once again powers it up. As the Alone prepares to fire at Wakaba and Himawari, Akane's Naked Rang suddenly activates, giving Aoi a boost and allowing her to defeat the Alone. Akane soon makes a recovery from her injuries, much to the relief of Aoi and her friends.

Wakaba decides to take Himawari shopping with her, putting her in a cute dress that starts attracting a lot of attention. When they are approached by a photographer wanting to photograph Himawari for a fashion magazine, Wakaba pushes her to give it a try, despite her lack of interest. When the photos get some good feedback, with the editors wanting her to go pro, Himawari gets upset at Wakaba when she books a shoot for a day when she promised to take her to see a factory. Himawari decides to attend the photo shoot on the condition that Wakaba be her servant for the day. However, she becomes panicked when she learns that the photographers changed her hairpins that Wakaba gave her whilst she was sleeping and starts searching the ocean for them. Thankfully, Wakaba had kept them safe for her and manages to return them to her. Just then, they are called in to fight an Alone planning to charge into the Manifestation Engine from outside the Earth's atmosphere. Working together, Wakaba and Himawari manage to hold off the Alone's attacks so Akane and Aoi can attack it with Vivid Blue. After the battle, Himawari makes plans to have Wakaba hang out with her for a whole day whilst Rei, who was unable to power up the Alone in time, becomes more desperate.

As Rei stakes everything on the arrival of the next Alone, which she plans to power up using her remaining arrows, Kenjirou learns of the source of the Alone's power-ups thanks to Himawari's analysis skills. The next morning, Rei goes to Akane's place to apologise for her behaviour the other day and is invited to have dinner with her and Momo. Meanwhile, Kenjirou tells Yuuri about how the Alone are linked to the accident that occurred seven years ago. Rei enjoys the evening as she has dinner, takes a bath and spends the night, and hears from Akane as to why she wanted to become her friend, making a promise that they'll stay friends. The next day, after Rei goes off on her own and Akane and the others are informed of a strategy to pinpoint the source of the arrows, another Alone appears, which Rei powers up with another arrow. Before she can fire anymore however, she is located by security droids and is forced to retreat, allowing Akane and Wakaba destroy the Alone. As Rei becomes cornered, she is discovered by Akane, both becoming shocked upon learning of each other's identities. Jumping to the conclusion that Akane knew her identity from the start, Rei feels betrayed by Akane, believing her wishes of friendship to be a lie, before she is captured by the military.

As Rei is put under high security whilst Kenjirou looks into her origins, Akane and the others are forbidden to talk with Rei, learning from Mizuha that she comes from another world. Wanting to see Rei again and learn the true story, Aoi and the others decide to break into the facility where Rei is being held. Reaching the holding cell, Akane conveys her feelings to Rei, pushing through with her desire to get to know her better. As Rei eventually accepts Akane's feelings, the crow, who reveals her name to be Daivesha, appears before them. Rei reveals her world was destroyed by Manifestation energy, being told by Daivesha that she could bring it back if she destroyed the Manifestation Engine. The whole thing is revealed to be a test by the Alone to see if they are worthy of wielding Manifestation energy. It is revealed that Daivesha had a trap set which would destroy the world if Rei was killed, but Kenjirou had believed in Akane's friendship and avoided that. Just then, Daivesha devours Rei, using the remaining power she had to evolve herself into her ultimate form.

As the crow starts rampaging with her new power, Kenjirou deduces that Rei is still alive within the center of the Alone she has become. With the crow taking off to head towards the Manifestation Engine, Akane finds Rei's key, which she believes may hold the key to their victory.