At the playground, Suneo, Tomokazu Seki proudly shows off Micross, his new radio-controlled toy robot, and Nobita, Megumi Oohara feels a sting of jealousy. He begs Doraemon, Wasabi Mizuta, to conjure a giant robot that could outshine Suneo, but Doraemon refuses, sparking a heated argument that drives him to slip away through the mysterious Door to the North Pole. Nobita follows and stumbles upon a bowling-ball-sized mechanical orb that can summon parts for a colossal machine. Back home, the orb is brought inside, and Nobita and Doraemon hatch a plan to build the robot in a hidden mirror world accessible by Doraemon’s Opposite World Entrance Oil placed on a calm surface of water.
The assembled giant robot seems to lack a brain, so a psychic controller is used to pilot it. Nobita and Doraemon name the machine “Zanda Cross” after Santa Claus, a nod to the North Pole discovery during their adventures with Shizuka, Yumi Kakazu. Shizuka is invited to participate and, when handed the psychic controller, she accidentally fires lasers that smash a skyscraper, revealing that Zanda Cross is not a toy but a weapon of war. Realizing the danger, the friends abandon both the robot and the mirror world, vowing to never speak of them again.
Meanwhile, a mysterious, scantily-clad girl named Lilulu begins tracking Zanda Cross from the North Pole to Nobita’s world. She reveals that she is the true owner of the robot, which she calls Judo, and Nobita reluctantly leads her to its location in the mirror world, handing over the psychic controller. Lilulu offers to forgive Nobita for taking the robot, but asks him to keep their secret.
That night, Nobita sneaks back into the mirror world and discovers Lilulu leading a group of robots who are constructing a large facility. He also finds Doraemon following him, troubled by Nobita’s recent despondency. Nobita explains what happened with Lilulu and voices his fear that she might be an alien. The two learn that the robots are preparing an invasion of Earth, so they escape back to the real world. Lilulu and Zanda Cross pursue them, but Zanda Cross is too large to fit through the portal and ends up destroying it, trapping the robot army in the mirror world. Nobita and Doraemon rejoice, feeling they may have saved the Earth—at least for now.
The next day, Doraemon discovers the orb beeping incessantly. Using his Translation Jelly, he learns that the orb is actually Judo, the mechanical brain intended to pilot Zanda Cross, and Judo reveals that the rest of the robot army has already been signaled to invade Earth.
With no adults believing their story, Nobita and friends recruit Suneo, Gian, and Micross (whom Doraemon has given sentience and the ability to talk) to help stop the invasion. They reprogram Judo with Zanda Cross so it can become an ally, and they create another mirror-world entrance by using the World Entrance Oil on Shizuka’s bathtub. Shizuka also ends up in the mirror world and finds an injured Lilulu, who is revealed to be an android. Lilulu tries to kill Shizuka when she discovers the truth, but is knocked out by Micross.
Lilulu shares the history of her home planet Mechatopia, explaining how robots were created by God after He supposedly gave up on humanity. The robots eventually rebelled, and in a compromise they decided to invade Earth and enslave humanity. Shizuka notes the parallels with humanity’s own violent past, which angers Lilulu, who attacks before collapsing from her injuries.
Meanwhile, Nobita and friends devise a plan to lure the robot army into the mirror world by using Zanda Cross’s signal and guiding them through a lake entrance. The invasion begins across major cities, but the army finds the cities empty and the humans nowhere to be found. Lilulu escapes and meets the army’s leader, but she implores them to end the invasion, arguing that humanity and robots are not so different. The leader condemns her, but Nobita and Doraemon rescue her.
The robots finally realize the ruse when they discover the world is backwards. They gather at the lake entrance to return to the real world, where Nobita and friends await them for a final showdown. Meanwhile, Shizuka, Lilulu, and Micross stay behind and use Doraemon’s time machine to travel back to ancient Mechatopia to plead with God to rewrite history. They meet God, an elderly figure, who agrees to reprogram the two progenitor robots Amu and Imu so that Mechatopia’s history can be rewritten. Lilulu volunteers to carry out the changes, fully aware this will erase her own existence.
Back in the present, the battle sways in Nobita’s favor as the invaders begin to disappear. In Mechatopia of the past, Lilulu fades away, sharing a final handshake with Shizuka before she is erased from existence. A heartbroken Shizuka and Micross return to the present and tell their friends what happened to Lilulu.
Some time later, Nobita, after school, glimpses Lilulu flying outside the window. As the end credits roll, he rushes to tell his friends, insisting that Lilulu has become an angel. They remain skeptical, but Lilulu’s silhouette soars into space, waving goodbye to Earth before continuing on.
