Hours late, Ichigo arrives at the meeting place. At first, she thinks Masaya has left, but he appears near her and tells her that he was waiting for her and that he loves her. Ichigo's cat ears pop out, but she hides them with a handkerchief and tells him that she loves him too. The next day, while Masaya is visiting the café, the aliens attack in search of the mew aqua rod. Ryou gives Masaya a sleeping drug to knock him out so the girls can fight. Kish is able to get the rod, but Keiichiro says the rod does not have any mew aqua anymore anyway. After the aliens leave, everyone begins cleaning the café. Outside, Ichigo bends over the sleeping Masaya and thinks about kissing him. She gets excited and instead of her ears and tail emerging, she turns into a small black cat.

As a cat, Ichigo gets lost while trying to escape from a large amorous cat. She finds herself standing in front of Masaya's house, where he discovers her and takes her inside. That night while he's asleep, she decides to kiss him, but accidentally kisses his dog instead. The kiss turns her back into a human, but before she can escape out a window, the dog licks her and she changes back into a cat again. Outside the house, the large cat finds her again, but she is rescued by a small grey cat wearing a green bandanna. Ichigo falls into the river, but the cat saves her again and tells her his name is Alto before she loses consciousness. She wakes up back on land and in her human form with Ryou bending over her and Alto gone. Ryou tells her that she must defeat the aliens as soon as possible if she wants to stop turning into a cat. While taking her home, he apologizes to her though does not say why.

Ichigo meets a cat at the train station and discovers that, even in her human form, she can understand him. The cat, named Asano, later comes to the café, and tells her that he is searching for the cat he loves, a Lilac Point Siamese named Jacqueline whose owner moved away. The girls agree to help him find her, but learn that her owner has taken her to a cat fair to find her a fiancé. Asano speaks to her there, but she says she cannot leave her owner because she is his most precious memory of his late wife. When one of the other cats is turned into a chimera anima, Asano comes to Jacqueline's aid. After the girls defeat the monster, Jacqueline's owner decides to allow the two cats to be together.

Ichigo asks for advice on her relationship with Masaya from the school fortune-teller Mariko. At first, Mariko says Masaya is a bad person, but then says he and Ichigo are good for each other as long as Ichigo is honest with her feelings. The next day, Ichigo sees Mariko watching a soccer player named Shunsuke. Later, Mariko tells him that he should confess his feelings to the person he loves on Sunday in the park. Meanwhile, the aliens search for Mariko's crystal ball, believing it contains mew aqua. On Sunday, Ichigo sees Shunsuke in the park and ducks behind a tree, where Mariko is also hiding to see who he meets. Kish appears and tries to steal Mariko's spirit, but Shunsuke's jumps in front of her to protect her, so his spirit is stolen instead and turned into a chimera anima. The other Mew Mews arrive, along with the Blue Knight, and they defeat the monster, freeing Shunsuke's spirit. Mariko's crystal ball shatters, proving it was not mew aqua. Shunsuke tells Mariko that she is the one he was waiting for.

When Ichigo's father finds out that she has a boyfriend, he does not approve. He demands that Masaya defeat him in a kendo match before he will allow them to continue dating. Ichigo complains to her mother, who explains that her father loves her and just wants to protect her. Her mother also tells her that they too had to fight to be together when they were young. Ichigo rushes to stop the fight, reminding her father of the past and how her mother did the same thing for him. Though he does not want to face that his "little girl" is growing up, he grudgingly gives his approval of the relationship.

Mint surprises the other girls by inviting them to a tea party. When they arrive, they meet a spoiled, wealthy girl named Kanna, who declares that she is Mint's "eternal rival." A box arrives, containing something Mint wanted to share with everyone. Watching nearby, Kish believes it must be mew aqua and tries to take the box. Not realizing the danger, Kanna takes the box back. Kish unleashes a chimera anima and Mint rescues the girl from the monster. The others transform and fight the monster, but are losing until the Blue Knight arrives and reveals its weak point allowing Mew Ichigo and Mew Mint to defeat the monster. Afterwards, Kanna admits she has always envied Mint. The box is opened to reveal that it is a special tea that Mint wanted to share with her friends. They invite Kanna to join them, but she declines and promises to invite them to her house for even better tea.

While the Mew Mews are battling one of Tart's chimera animas, a young man named Yuebin Ron appears and defeats it with his bare hands. An apprentice of Pudding's father, he has come to spend a night competing with Pudding so that he can be the successor of the family's fighting style. He defeats Pudding, and tells her that she must also now become his fiancée. While talking, he accidentally knocks over Pudding's photo album and damages it. Upset, Pudding locks herself in the café where Tart attacks her. While the other girls are stuck fighting Kish and defeat his chimera anima, Yuebin rescues Pudding. Afterwards, Yuebin goes to China to continue his training so he can be strong enough to protect his future wife.

The girls participate in an open market where Lettuce sells a variety of dolls that she made herself, which are popular with the crowd. The last doll is purchased by famous doll maker Ayano Uemura who invites Lettuce to work with her at her workshop. Lettuce happily accepts and they make a doll together that Ayano takes to an exhibition. When the girls go to see the doll, they discover that Ayano took all of the credit for making it and denies that Lettuce helped her. Kish appears and steals Ayano's spirit to make a chimera anima. The girls transform and defeat the monster, returning Ayano to normal. Afterwards, Ayano confesses that she was envious of Lettuce's talent and had run out of new ideas. Lettuce forgives her, and tells her she does not care whose name is on the doll as long as it makes people happy.

Ichigo meets a lonely girl named Momoka whose parents are always busy. Ichigo learns she is a fan of Zakuro, so she tells Zakuro about the girl. Zakuro later runs into the girl at a restaurant. Momoka is upset at learning her parents have cancelled their dinner plans, but Zakuro assures her that her parents still love her and invites the girl to have dinner with her instead. The next day, Momoka's parents send her a beautiful pendant that Kish believes is made of mew aqua. When the daycare holds a family picnic, Momoka's parents do not show up and the upset girl runs off. Along the way, she loses the handkerchief that Zakuro gave her. Kish offers to help her, if she gives him her pendant. Zakuro arrives to help her, but is entangled in some vines by Kish. After realizing the pendant contains no mew aqua, Kish leaves. Zakuro returns the handkerchief and pendant to Momoka. Her parents arrive for the picnic, and Zakuro feels certain they will not leave her alone again.

Ichigo tries to talk to Ryou about the problems caused by her cat genes, but he ignores her. On the way to school, Ichigo changes into a cat again and gets in trouble, but is saved by Alto who also kisses her to change her back to normal. Despite his struggling, Ichigo picks him up and is shocked when he suddenly changes into Ryou. After school, she goes to the café where Keiichiro tells her the history of the Mew Project, which was started by Ryou's father. After his parents were killed by an ancient chimera anima, Ryou decided to continue his father's research. Wanting to be sure the merging process was safe, he tested it by merging himself with cat genes. This gave him the ability to change into a cat at will, but only for 10 minutes at a time or he will remain a cat permanently. Ichigo promises to do her best as a Mew Mew.

As Christmas approaches, Ichigo grows depressed as she thinks about how she is regularly lying to Masaya to hide her being a Mew Mew. Zakuro invites her to go shopping with her and tells Ichigo that since she cannot open her heart, she should give Masaya something that reflects her feelings. Ichigo chooses a necklace called "Tears for Christmas." She is still initially reluctant to face him, but finally arranges to meet him at the big Christmas tree in Odaiba. While she is waiting, the aliens attack. When Ichigo transforms, her emotions cause mew aqua to materialize at the top of the tree. Joined by the others, the Mew Mews prepare to fight the aliens to acquire it.

The aliens add more energy to the mew aqua, putting the area in danger of being destroyed. The Mew Mews are able to reduce the power of the explosion, however no one had noticed Masaya was nearby. He is hit by one of the fragments of the mew aqua and knocked unconscious. At the hospital, Ichigo watches over him and talks to him, telling him she is sorry for hiding the truth from him. As she cries, the mew aqua reacts and it begins snowing. Masaya wakes up and they return to the tree where Ichigo tells Masaya the truth about her being a Mew Mew. Masaya tells her that he already knew, and that it does not bother him. He pretended not to know because it was what she seemed to want. Ichigo gives him the necklace.

Pie creates a chimera anima capable of manipulating dreams. The monster puts Ichigo to sleep and reforms itself into a replica of her to go to the café and send the other four girls into Ichigo's dreams. They transform, but as the dream is being manipulated by the chimera anima, their attacks are sent back at them. They realize that they must wake Ichigo up to win, but are unable to do so. Kish suddenly stops Pie from killing Ichigo and wakes her up, freeing the others. After they defeat the chimera anima, Kish tries to kill Mew Ichigo, but he is still too injured from his last battle with the Blue Knight. Ichigo yells at the aliens, but they tell her they are fighting for their friends. The Mew Mews realize that the aliens do have their own feelings and something they are trying to protect, the same as them.

Masaya is having weird dreams in which an unidentified voice is telling him to wake up. Meanwhile, Pudding is watching performance at the Tokyo Dome when a huge hole opens in the floor. She transforms and investigates, finding Tart under the Dome. He tells her they are going to make the whole area collapse by having chimera animas dig holes under it, starting with the Dome. While showing off his monster, it goes out of control and leaves, trapping Mew Pudding and Tart inside by falling debris. Mew Pudding is happy, though, and tells Tart that since they are both trapped, they do not need to fight. She gives him some candy and starts calling him "Taru-taru." Outside, the other Mew Mews defeat the chimera anima then use their powers to keep the dome from collapsing while it is evacuated. Tart decides it would be boring if Pudding died, so uses his powers to make trees grow around the Dome so the roots support it. He teleports Pudding to the surface and she says they are friends now. He yells at her and leaves, but smiles while looking at the candy she gave him.

The aliens decide to use special chimera animas to release pollutants into Tokyo Bay. The Mew Mews arrive, sans Lettuce, and find themselves having to fight numerous smaller chimera animas made from fish. Mew Lettuce and Ryou arrive by boat, but the larger monster destroys it and they are thrown into the water. While the others defeat the fish monsters by combining Mint and Pudding's attacks, Lettuce tries to save the drowning Ryou. Her emotions activate the mew aqua around his neck, causing her legs change to a porpoise fin and easily bring Ryou back to the surface. The mew aqua weakens the remaining chimera anima, enabling them to defeat it.

Zakuro is offered a leading role in a movie in Hollywood, but this would require her to move to America. She has not decided whether to take the job or not, but she tells Ichigo that the girls still know nothing about saving the Earth and that she is losing patience with them. Meanwhile, Kish learns that the conditions on his planet have gotten worse and that he must hurry to find the mew aqua so he can save his people. The girls also renew their search for mew aqua, however when the aliens appear, Zakuro refuses to transform. Mew Mint is hurt while protecting Zakuro, but Zakuro does nothing. After the battle at the café, Ichigo complains to Ryou who acts indifferent. The girls decide to confront Zakuro about her behavior. Masha leads them to a church where they find Zakuro with Kish.

Kish tells the girls that Zakuro has betrayed them, and then invites Zakuro to join them. Ichigo yells at Kish, and he tells her more about Deep Blue, their "god" and that the mew aqua is needed to help him awaken, before teleporting away with Zakuro. Ryou calls the rest of the Mew Mews to a bird sanctuary, where they believe a swan is holding the mew aqua. As they try to figure out how to find the swan, all of the birds in the area gather near, realizing Mint can understand them. As the swan is about to bring them the mew aqua, the aliens attack but Mint refuses to transform. The swan flies up to her and honks at her, but Mint refuses to listen. It absorbs the mew aqua and flies away. Afterwards, she explains the birds were crying for help. Ichigo still believes Zakuro has not betrayed them; Mint says people change. That night at the café, Ryou reveals that Zakuro told him she felt they were still little girls, and not the true warriors they would need to be to protect the Earth. The girls rush off to the sanctuary to stop Mew Zakuro and Mew Mint, who have begun fighting one another. As Mew Ichigo tries to calm Mint down, a twister created by the alien appears that sucks in all the birds. Mew Mint flies into the twister and retrieves the mew aqua from the swan. Mew Ichigo uses its power to stop the twister and the aliens retreat. Zakuro apologizes and explains that she was bothered the girls were listening to rumors instead of believing in one another.

Ryou and Keiichiro learn that mew aqua may have been made by the aliens when they inhabited Earth. A strange type of energy begins emerging in Tokyo and trees grow out of control, turning the city into a forest. The Mew Mews find something that appears to be a large mew aqua in a tree but before they collect it, Tart arrives and turns the tree into a chimera anima. During the fight, Mew Ichigo realizes that Ryou cannot be the Blue Knight as they both appear at the battle to aid her. The Mew Mews defeat the monster, but they are unable to figure out what caused the forest to appear in the first place.

For Valentine's Day Ichigo decides to make chocolate for Masaya, with help from Keiichiro. On her way to meet him, she is attacked by Kish who knocks away her transformation pendant. Masaya senses that Ichigo is danger and comes to her rescue. After Kish injures him, Masaya begins glowing and transforms into the Blue Knight, however with the injury he is unable to fight at his full strength. Just as Kish is about to kill him, Ichigo grabs her pendant and runs in front Masaya to block the attack using a shield from the pendant. Ichigo rejects Kish and he leaves. Later, as Masaya enjoys the chocolates from Ichigo, Kish wonders who or what Masaya and the Blue Knight really are.

Masaya begins having prophetic dreams, including one where he is invited to join the team and one where he sees Ichigo crying. The next day, his first dream comes true, against Ryou's protests and Zakuro's concerns, and he becomes a member of the Mew Project. The group goes to investigate a strange light being emitted from a river to determine if it is mew aqua. The aliens also go to the river. As the two groups battle, Mew Pudding and Tart both jump into the river to look for the mew aqua, eventually discovering there is none. After Mew Ichigo uses her attack to increase the Blue Knight's sword's power, he destroys the many chimera animas being used by Pie. The light disappears and the aliens leave as the Mew Mew wonder what is going on.

Deep Blue orders the aliens to destroy the Blue Knight. They decide to kidnap Mew Ichigo in order to draw him out. Meanwhile, Ichigo is happy to have Masaya now working at the Cafe Mew Mew. The next day, the aliens attack with a chimera anima that resembles a large octopus. Masaya, as the Blue Knight, joins the Mew Mews in the battle. The creature captures the Mew Mews and the Blue Knight is forced to drop his sword when Pie and Tart threaten to kill Ichigo. It is able to capture the Mew Mews, including Ichigo, in its arms. Pie and Tart force the Blue Knight to kill Ichigo. The aliens then repeatedly attack him, but before they can kill him, Mew Ichigo suddenly breaks free and attacks the aliens with an unbelievable new power. As Pie and Tart flee, the nearby Kish wonders where the power came from, as he is certain it did not come from Ichigo.

The group is searching for mew aqua around a large rock formation in the forest when the girls and Masaya get separated. Something strange begins happening and everyone transforms. Masaya transforms into the Blue Knight, but falls from the rock and returns to normal. Kish confronts him and reveals that he cannot maintain his Blue Knight form if he is not protecting Ichigo. The alien moves to kill Masaya, but Mew Ichigo transports and appears between them. Masaya is knocked unconscious as Kish tries to kill Ichigo. This triggers Masaya's transformation, but his powers go out of control due to his rage at Kish. The other Mew Mews teleport to Mew Ichigo just in time to put up a shield around her as the rock explodes from the Blue Knight's power. Masaya returns to normal, seemingly unharmed. Kish tells Pie and Tart that the Blue Knight is the one who can save them.

Ryou and Keiichiro tell the girls to take a vacation, feeling the final battle is approaching and wanting them to be refreshed. Ichigo, however, cannot find Masaya to enjoy the downtime with. Meanwhile, Kish tells Pie and Tart that he is going to use the Blue Knight's powers rather than waiting for Deep Blue to awaken. Pie disagrees, but Tart is convinced. They release all the chimera animas they have in order to distract the Mew Mews and the Blue Knight, while the aliens search for Masaya. Ryou realizes it is a trap and sends the Mew Mews to find Masaya as well. When the girls eventually find him, he is lying unconscious. Mew Ichigo approaches him, but he transforms into the Blue Knight. All of the strange energy in the city gathers around him and he transforms again, into Deep Blue.

As Ichigo stands in disbelief that Masaya is Deep Blue, Pie explains why they have been waiting for him. Ichigo tries to reach Masaya, showing him the bell collar, but it is useless. Unable to fight him, the other Mew Mews rush to protect Ichigo as the alien attacks her, eventually being wounded enough that they are forced back into their human forms. When Deep Blue uses his sword to destroy Tokyo, Ichigo finally realizes he is not Masaya anymore and attacks, but he is too strong. Ryou arrives and protects her from his attack, then tells her that everything is just as the Earth wanted it to be, that the planet chose her and the other Mew Mews to protect it. Her determination renewed, the final battle begins.

Deep Blue teleports to his base, where Keiichiro detects the final mew aqua. Pie creates a chimera anima similar to the one that killed Ryou's parents. As the Mew Mew's battle, Mew Ichigo tries to reach Deep Blue's base. Pie goes after her, but Tart protects her and is killed by Pie. Ichigo reaches the room with the mew aqua just as Deep Blue does and he attacks. Kish appears and pretends he is going to kill Mew Ichigo, but instead teleports right in front of Deep Blue and tries to attack. Deep Blue dodges the attack and kills him. Kish dies in Ichigo's arms as she cries, mirroring Masaya's prophetic dream. Deep Blue begins screaming and releasing tremendous amounts of energy. It knocks Ichigo unconscious and destroys all of the chimera animas and everything else around the base. Pie uses his fans to protect the Mew Mews, at the cost of his own life. Inside the base, Mew Ichigo comes to and finds Deep Blue standing in front of her. He drops his sword and calls her by name, revealing Masaya has regained control of the body.

Masaya and Ichigo realize that the final mew aqua is inside his body. Deep Blue's spirit remerges, despite Masaya's attempts to regain control. Eventually, Deep Blue wins and claims to have destroyed Masaya completely. He goes to activate the mew aqua so he can destroy the Earth. Masaya's spirit emerges from his body, pulling Deep Blue's spirit out as well. He tells Ichigo to attack, knowing it will kill both of them. Before he dies, he tells Ichigo he wanted to save the Earth and that he loves her. With Deep Blue's death, the mew aqua is released, healing the destroyed city, the Mew Mews' wounds, and reviving the dead aliens. Masaya's body is returned to normal. Unwilling to let him die, Ichigo kisses him and gives him all of her power. Masaya awakens to find Ichigo lying beside him, dead. The other Mew Mews teleport into the base and begin crying over her death. They suddenly return to their normal forms as the base begins to fall apart. Kish appears with the last of the mew aqua. Pie and Tart also come and they thank the girls before teleporting them safely to the ground. The three aliens destroy the base to prevent it from falling on the city, then leave to return to their own world. Masaya kisses Ichigo. She detransforms and wakes up, to everyone's delight. The girls believe that they have lost their powers permanently, but discover that they only faded temporarily and are told that they have a new enemy.