Mewtwo is flying with a group of Flying-type Pokémon over a mountain range, and later, the ocean. Deciding to challenge the limits of its power, Mewtwo flies ahead, Mega Evolving into Mega Mewtwo Y and ascending into the sky. Meanwhile, the Genesect Army arrives at a snowy area that their leader, a Red Genesect, believes to be their home. Confused and distressed, the Genesect carrying theDouse Drive calls out "I want to go home."
Mewtwo reaches the atmosphere but realizes it cannot stay there and begins falling. After changing back to its ordinary form, Mewtwo hears the Douse Drive Genesect's plea and rushes off to find them. An avalanche begins, and Mewtwo arrives in time to save the four regular Genesect, but the Red Genesect is swept up in the snow. Mewtwo peers into the Douse Drive Genesect's mind and learns that they were resurrected from three-hundred-million-year-old Fossils by Team Plasma but escaped, and they are now searching for their home and see everyone around them as enemies. The Red Genesect returns and attacks Mewtwo, initially out of a belief that it was threatening the other Genesect but later out of anger over learning that their home is gone due to the passage of time. Mewtwo watches as the Genesect Army flees. Later, the five Genesect discover a large city's skyline, and seeing it as similar to their home, the Douse Drive Genesect happily says "I'm going home."
AshIris, and Cilan arrive in the central area of New Tork City and visit the Pokémon Hills nature park. Their guide, Eric, shows them around, and their Pokémon play with the wild Pokémon in the area for a while. Later, however, Pikachu sees the Douse Drive Genesect sitting at a pond and staring at flowers floating on the water. The Genesect becomes frightened and folds up, leading Ash to sit on it in the mistaken belief that it is a statue. It flies off with Ash riding on it. After landing, Ash strikes up a friendship with the Genesect, and it tells him that it wants to go home. Ash realizes this means that it is lost and promises to somehow help it get back home. Suddenly, the Red Genesect and Shock Drive Genesect arrive. Perceiving Ash's petting the Douse Drive Genesect as harming it, they attack. The Douse Drive Genesect tries to stop them, but using its power, the Red Genesect forces it to attack its new friends. However, Mewtwo suddenly appears and protects the humans from the attack, and the Genesect leave.
In an underground tunnel, Ash, Iris, and Cilan thank Mewtwo for saving them, but it says it was only protecting Pikachu and Axew. Ash insists that Mewtwo tell them what kind of Pokémon they had encountered, so Mewtwo reveals that they are Genesect, Pokémon who were extinct for 300 million years until humans revived them from fossils. Mewtwo explains that it identifies with them due to its own origins as a Pokémon created by humans, then tells the group to forget they ever met it and flies off. Team Rocket, who were eavesdropping on the conversation, decide to catch both Mewtwo and the Genesect Army.
At the Pokémon Center, Ash spots a photo of the flowers he had seen the Genesect looking at. Eric explains that they are an ancient species known as the Panna Lotus, which he transplanted fromAbsentia Natural Park to Pokémon Hills. That night, while Ash, Iris, Cilan, and Eric eat at the Pokémon Center, the Genesect begin rampaging in Pokémon Hills, driving all the Pokémon out of the park. Once they have the area to themselves, the Genesect begin spinning a giant cocoon from sturdy threads, but the thread reaches underground into a power station, disrupting the power to the city. Team Rocket sneaks into Pokémon Hills, and Ash and the others rush there after being warned by a Sableye they befriended earlier only to discover all the Pokémon outside as a result of the Genesect rampaging. Cilan returns to the Pokémon Center to help an injured Ralts. Ash, Eric, and Iris try to enter but the Shock Drive and Chill Drive Genesect push them away, so Eric shows them a workers' corridor used as an alternate entrance. Meanwhile, Team Rocket attempts to capture the Genesect with a bazooka but the Red Genesect spots them and drives them off. The tunnel leads Ash, Iris, and Eric to the underground power station, where they discover the threads wrapped around the generators.
Standing on a bridge overlooking the city, Mewtwo muses about its own origins. It flashes back to its creators conceiving it in a tank and later torturing it during an experiment, at which point it escaped. As it recalls how it once thought it was alone, it then flashes back to being badly injured after a violent battle and being struck by a bolt of lightning, at which point it encountered a cave of wild Pokémon that took it in and cared for it. Having realized it wasn't all alone after all, Mewtwo concludes that the Genesect deserve the same. A pair of Starly arrive and inform Mewtwo of the Genesect Army's rampage in Pokémon Hills, so it sets off.
Ash, Iris, Cilan, and Eric reach the main area of Pokémon Hills and are approached by the Douse Drive Genesect, who apologizes for attacking them earlier, leading Ash to conclude that it couldn't refuse the Red Genesect's orders. The Douse Drive Genesect excitedly runs to a pool where it shows them the Panna Lotuses and tells them that it likes the flowers, which grew in its home. Iris realizes that the cocoon is the Genesect Army's nest and that they are trying to turn Pokémon Hills into their new home. When the lights begin flickering again, Eric realizes there is an emergency at the power station and rushes off to resolve it, for if it continues, the station will explode, blacking out New Tork City and sending it into chaos. A Feraligatr native to Pokémon Hills starts fighting with the Red Genesect after breaking part of the cocoon, and when the Red Genesect uses Blaze Kick to knock the Feraligatr off a ledge, Mewtwo appears and rescues it with Psychic.
Mewtwo warns the Red Genesect not to attack the other Pokémon but it refuses to listen, so Mewtwo leads it out of Pokémon Hills while the Chill Drive, Shock Drive, and Burn Drive Genesect begin attacking Ash, Iris, and the other Pokémon. Cilan returns to help, and the Douse Drive Genesect manages to resist the order to attack when it hears Ash's voice. The Red Genesect attacks Mewtwo as they fly through the city, ultimately forcing Mewtwo to fight back by ignoring all of Mewtwo's warnings. Mewtwo Mega Evolves and the two engage in a high-speed chase throughout the city. At Pokémon Hills, the other Genesect fight the wild Pokémon and eventually become overwhelmed, at which point the Red Genesect returns to protect them. When the Red, Burn Drive and Chill Drive Genesect turn to attack a Persian, Ash runs between them in an attempt to stop the attack, the Douse Drive Genesect jumps in the way and takes the full force of its allies' power. After expressing gratitude for Ash being safe, the Douse Drive Genesect's eyes go dark.
The other four Genesect take an aerial formation and begin to attack the rest of the Pokémon, but Mewtwo arrives and shields them with Protect. Mewtwo gives the Genesect Army a final warning to stop their rampage or be defeated, which the Red Genesect ignores. All four remaining Genesect engage Mewtwo in battle around the cocoon but are largely unable to keep up, especially when Mewtwo Mega Evolves to increase its speed. To counter this tactic, the Red Genesect orders the other three to try dragging Mewtwo down with their threads, but Mewtwo breaks free using Psystrike. The three regular Genesect fall through into the power station, causing the generators to completely overload, igniting fires on the cocoon's threads and blacking out all of New Tork City. Team Rocket, wandering around in the dark, fall into a work site and land on a group of Durant, who blast them off with Hidden Power.
As Mewtwo and the Red Genesect speed around the cocoon in pursuit of each other, the fires on the cocoon spread. The Douse Drive Genesect wakes up and attempts to stop it, and Oshawott, Feraligatr, and the other Pokémon help it. The other Genesect climb out from the pit only to be trapped by the flames, but they are freed by Persian's Water Pulse. They then return the favor by protecting Ash from a falling piece of debris, having lost their aggression. The Douse Drive Genesect, however, is suddenly caught in a burst of fire and falls unconscious again. Up above, the Red Genesect manages to get in a hit on Mewtwo, nearly sending it falling into the fire; however, Ash, Iris, and Cilan catch it. Shifting back to its ordinary form, Mewtwo lands, as does the Red Genesect. After one last exchange of attacks, Ash runs between them and attempts to convince them to stop fighting. The Red Genesect refuses to listen and begins charging a Techno Blast at Ash, but the Douse Drive Genesect wakes up again and weakly begs its leader to stop. It is soon joined by the other Genesect and the Pokémon Hills Pokémon, but the Red Genesect refuses to let go of its quest and now declares even its own kind to be its enemy, firing its Techno Blast.
Mewtwo has had enough. It Mega Evolves, blocks the Techno Blast, restrains the Red Genesect with Psychic and grabs it by the cannon before shooting up into the sky, declaring that they must go beyond the limit, where nobody else exists. It blacks out after flying so high that they both begin to freeze. A short time later, Mewtwo wakes up alongside the Red Genesect in the upper atmosphere. The Red Genesect is in awe of the planet, and Mewtwo explains that it is the planet where they were both born, that they exist for a reason, and that on this planet, they are all friends. The aggression fades from the Red Genesect's eyes, and it accepts the hand extended by Mewtwo as an invitation to return to their home. However, as they fall, Mewtwo blacks out again. The Red Genesect grabs Mewtwo and uses its last powers to send a signal to the other Genesect to "return home" before blacking out as well.
As the last of the fires on the cocoon is put out, the other Genesect get the signal that the Red Genesect and Mewtwo are falling and fly off to help. Ash sends out Charizard and Iris sends out Dragoniteto aid them. The Genesect create a net of thread to catch the two falling Pokémon, and Dragonite and Charizard try to hold it up, but their efforts fail. Ash declares they will catch Mewtwo and Red Genesect themselves, and on a suggestion from Iris, all the Pokémon create a giant cushion of water to catch them. Mewtwo helps the Red Genesect up from the water, and it voices its newfound belief that everyone is its friend. As everyone expresses relief that the crisis is finally over, Ash spots the Panna Lotuses and realizes that he knows where the Genesect can go.
Eric takes Ash, Iris, Cilan, and the Genesect Army to Absentia Natural Park, a place where the Panna Lotuses still grow naturally. While the other Genesect build another cocoon there, the Douse Drive Genesect happily tells Ash that it likes its new home. Mewtwo then thanks Ash for helping find the Genesect a home and tells him it will always be grateful that they met before Mega Evolving and flying off. Ash, Iris, and Cilan express hope they will meet Mewtwo again someday.
In the credits, the Genesect complete their nest in Absentia Natural Park. Eric is seen guiding a tour of the completed Pokémon Hills now that it is open to the public. Many rivals from the Best Wishesseries go by, as well as AlderIngoEmmetCynthiaProfessor JuniperCedric Juniper, and Don GeorgeN is shown walking alone in a polar area. Ash, Iris, and Cilan walk past a disguised Team Rocket at a café. Mewtwo arrives in another large city at night and lands on a building, overlooking the vast metropolis.