The story takes place in an alternate reality based in the year 1996, where humanity is advanced enough to develop long-range space travel, as well as bases on both the Moon and Mars. However, the Cold War tensions between the United States and the Soviet Union have not ended; rather, they've escalated as both sides build military facilities in space, and the shadow of nuclear conflict looms over humanity, both on and off Earth. Meanwhile, on the Red Planet, an exchange program created by the United Nations to promote peace and understanding is about to begin; the "Cosmic Culture Club," consisting of 16 boys and girls, as well as their instructor Elizabeth, arrives at the UN Mars base. Among the passengers is Anna a 14-year-old girl who serves as the narrator for the story. Suddenly, four unidentified humanoid robots classified as Super Powered Tracers are detected, engaged in fierce combat with each other. The UN base is caught in the crossfire and quickly destroyed, killing all but six members of the "Cosmic Culture Club"—Elizabeth, Arthur, Roan, David, Simone and Anna, and leaving them stranded on an inhospitable planet that has suddenly become a battlefield. As the battle ends, the lone SPT standing lands next to the terrified group and opens up revealing a pilot, who simply announces to them, "Earth is at stake."

Love Momozono is a 14-year-old student at Yotsuba Junior Highschool that tends to care more for others than for herself. One day she visits a show of the famous dance unit "Trinity" and decides to become a dancer, too. On the same event, subordinates of the Labyrinth Kingdom show up who want to collect the unhappiness of the audience. Love gets the power to change into Cure Peach and fights them. Soon after, she is joined by her good friends Miki, who is Cure Berry, and Inori, who becomes Cure Pine. (Source: ANN)

After Leader X is seemingly destroyed for good at the end of Gatchaman II, a fragment of him that survived grows and mutates into Z. With the head of the Egobossler family, Count Egobossler (and his two subordinates Mechandol and Kempler), Z is bent on destroying the Earth, and the Science Ninja Team, once more. In the wake of Anderson's death, Dr.Nambu has become the new head of the ISO, while the team is now confined to the Gallatown (aka "G-Town") underwater base. Engineer Kamo is introduced, and after the New GodPhoenix is destroyed early on, the team receives the new Gatchaspartan as their mecha. The Gatchaspartan has a special mode as well, called Hypershoot, that can only be utilized by Ken (with his new "Gatchafencer" sword). As the series progresses, it is learned that the radiation exposure from constant use of the Hypershoot is slowly killing Ken, and that continued use would mean death. Meanwhile, Z plans to destroy the earth with an antimatter asteroid, codenamed "Poison Apple".

Middle schooler Mana Aida is known for her vivid passion and kind-hearted disposition, especially by her friends Rikka Hishikawa and Alice Yotsuba. While the girls are on a school field trip, otherworldly villains from the "Trump Kingdom" appear and create giant monsters from the civilians' selfish desires to cause havoc. In the midst of finding a way to stop the destruction, Mana encounters "Cure Sword," a mysterious Precure warrior. As Cure Sword engages in combat with the monsters, Mana meets Cure Sword's fairy allies, who tell her that she also has the ability to transform into a warrior herself. When Trump Kingdom's invaders begin to outnumber Cure Sword, Mana takes to the battleground with resolve. She partners with Sharuru, one of the fairies, and transforms into "Cure Heart"—the Precure of Love. In her attempts to ally with Cure Sword, Mana ends up pulling Rikka and Alice into the fray, whom each partner with a fairy ally to transform into "Cure Diamond" and "Cure Rosetta," respectively. Together, they battle against the Trump Kingdom invaders to protect the love in the world from being destroyed. [Written by MAL Rewrite]