Alice and Kazumi are two friends who aspire to become great detectives like Milky Holmes. Whilst on a day out, they spot a thief and decide to pursue him. Although his escape is thwarted by the arrival of Milky Holmes, he is retrieved by other members of a group of thieves calling themselves Colors Phantom.

Alice and Kazumi decide to sneak into Holmes Academy for a chance to see Milky Holmes, where they end up getting inadvertently knocked out by them. As the two state their desire to be just like Milky Holmes, they simply respond by saying if they want it, they should just do it, whilst trying to keep up a classy image. Later that night, Alice and Kazumi encounter the thief from before, donning their new detective uniforms to fight against him. Whilst Kazumi's Arrow Toys prove to be ineffective, when combined with Alice's Barrier Toys, they combine into a powerful arrow that knocks the thief out. The girls leave the thief in the custody of the police, leaving behind a calling card naming themselves "Feathers".

After Blue Phantom retreats upon the arrival of Milky Holmes, Kazumi is downhearted that her Toys were unable to respond. Whilst heading to ask Milky Holmes for advice again the next day, Kazumi comes across a staircase leading to a mysterious room containing logs of the times Milky Holmes had lost their toys, helping her to realise more than one Phantom was involved the previous night. Later that day, they manage to trap Ryuko, who is revealed to be one of Color the Phantom, Yellow Black Hole. As the Blue Phantom joins the attack, Alice deduces the powerful arrow Kazumi shot the other day comes from combining their Toys together, knocking back Blue Phantom and revealing him to be a TV presenter. Ryuko leaves a cryptic message for Alice and Kazumi before escaping with Blue Phantom.

As Alice and Kazumi take up part-time jobs to fund their Feathers activities, Alice takes note of an old lady who seems to come to the same bar by every day. Curious, they decide to follow the old lady on the bus and eventually runs into her, where she tells them about she often goes on the bus to meet someone. The next day, Alice and Kazumi notice something off when they spot the old lady going off with the bar master, deducing the master has deception Toys that allow others to perceive her as different people, revealing her to be a phantom thief named La Lunar, who Alice and Kazumi manage to defeat. After the thief is arrested, the girls realise the person the old lady keeps meeting with is the bus driver, her son.

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Alice's parent confront her older brother, Shion, who, unbeknownst to Alice, is Color the Phantom's leader, Violet Shadow. Meanwhile, Ryuko leads Alice and Kazumi into a trap, but Alice manages to see through her trickery and defeat her. As Ryuko is taken into custody, her two associates, who had been monitoring their battle, shows Shion the true identity of the Feathers.

Alice and Kazumi are called over by Milky Holmes to meet Ellery Himeyuri, who had previously helped them during a case years ago, asking them to let her stay at Alice's house during her last night in Yokohama. Ellery spends the evening with Alice and Kazumi, where she reveals she knows their identities as Feathers. That night, they learn of a French thief named Monseur Miller, who uses his Toys to make duplicates of himself out of mirrors. Using her own Induction ability to copy Alice's Toys, Ellery manages to stop Miller by using Alice's shields to deflect Kazumi's arrows. As Kazumi grows concerned that Alice is much stronger than she is, Kokoro's police partner Keiko Totsugawa, who is secretly one of Color the Phantom, takes a picture of the Feathers and learns about Alice being Shion's brother.

Keiko appears before Shion and Visconte, using her Toys to wipe their memories of their encounter. As Kazumi's continues to be downhearted that her Toys are allegedly weaker than Alice's, Color the Phantom announce their intent to steal Visconte's 'most important treasure'. Keiko arranges for Alice and Kazumi, Visconte and his wife, Madame Visconte, Shion and Milky Holmes to the top of a skyscraper. There, Shion reveals his identity to Alice, attempting to recruit her as a phantom thief, but Kazumi suddenly steps in, deciding to become a thief in Alice's place.

As Kazumi ends up joining Color the Phantom, going against Keiko's calculations to have Alice join, Alice discovers a hidden room in her house, confirming her parents are also phantom thieves. Keiko decides to test Kazumi's resolve by having her Opera Kobayashi's cap, but she is unable to go through with it. After pointing out that Kazumi had only joined out of inferiority to Alice's powers, she escapes, leaving Kazumi alone to fight against Milky Holmes. However, Alice steps in to protect Kazumi, telling her she is willing to become a thief as well in order to stay with her. Realizing that what she wanted all along was to stay by Alice's side, Kazumi decides to return to being a detective.

Shion assembles all the members of Color the Phantom, including those previously captured, announcing that he intends to disband the group. However, he is apprehended by Great White Doom Angel and Darkside Revolution, who assume control of the group and launch an attack on the city to lure Alice and Kazumi out. Arriving at the tower, they are not only assisted by Kokoro and her Genius 4 Unit, but are also helped by Arséne and her Gentleman Thief Empire. They soon come up against Doom Angel and Darkside, who seek to claim Shion for their own and attack with their Toys, but are soon joined by Milky Holmes.

Whilst Milky Holmes fights against a demon created from Doom Angel and Darkside's Toys, Alice and Kazumi head to the rooftop, where they find the two planning to unleash a giant ball of energy destroy Yokohama. However, their Toys go out of control and suck themselves inside the ball. Believing in their own strength, Alice and Kazumi use their combined toys to destroy the ball, whilst Shion manages to save Doom Angel and Darkside using his own Toys of flight. As the incident comes to a close, some of Color the Phantom begin new lives, Milky Holmes decide to take Alice and Kazumi under their wing as Milky Holmes Feathers.