The base is described by Pie as Deep Blue's "final weapon". It gets its power from the final Mew Aqua, as it is said to amplify Deep Blue's powers. The base appears as a dark blue diamond-shaped object, with white rectangular objects surrounding it. With it, it also features four long arm-like structures surrounding it as well.
As the final battle rages, Deep Blue summoned his floating base high above the ruins of Tokyo, and he then ordered Pie to handle the Mew Mews. Ichigo Momomiya and the others battle Pie, but he summons a Chimera Anima, which looks like the one who killed Ryou Shirogane's parents years ago. Ichigo headed up to the base, but Pie attempted to stop her by using his fan. He was stopped by Zakuro Fujiwara, and then blocked by Tart's weapon, and he tells Pie that he doesn't want to fight the Mew Mews anymore, so Pie kills him. Ichigo is able to enter the base, where Deep Blue is expecting her to arrive.
Meanwhile, at Cafe Mew Mew, Keiichiro Akasaka discovered that the final Mew Aqua was inside the base. As Ichigo enter the very place where Deep Blue waited, he launched an attack on her, and she dodged it. However, Quiche interfered, and knelt down before Deep Blue, apologizing to him. Deep Blue asks if he seek forgiveness, but Quiche teleports, and put his weapons by him, which he was trying to kill Deep Blue with, but Deep blue impaled Quiche in the torso, and threw him into Ichigo's arms. She cried over Quiche's death and Deep Blue triggered the final Mew Aqua from within the base, sending a blast of energy down to Tokyo. It destroyed many of the Chimera Animas in the process. However, as the surging blast comes towards the Mew Mew, Pie appears and smiles at the Mews, using his fans to save them, while ultimately sacrificing his life.
Afterwards, as the Mew Mews and the others are knocked down, the city is reduced to ruins. Inside the base, Masaya Aoyama reawakens from within Deep Blue, who then blames himself for what he had done. Ichigo then tells him that it was only Deep Blue that did this, and he thanks her. The two hug which cause the Mew Aqua from within Masaya to come out, telling her that he can use it to save the people and the world.
Suddenly, Deep Blue reawakens, and grabs Ichigo by the neck, telling her that Masaya's body and the Mew Aqua within him is his. Ichigo and Deep Blue battle until Masaya emerges from him, and tells Ichigo to finish him off. Then, with the aid of the other Mew Mew's powers, Ichigo gives the final blow and destroyed Deep Blue once and for all. The base begins to collapse, but the Aliens use the last of the Mew Aqua, sending down to safety. Then the three remaining aliens use the ship, and destroy the base before it makes an impact on Tokyo, and leave the Earth to return to their home planet.