The movie begins with the world of Pokémon opening, showing the Unova Pokémon populating the land, seas and skies. The screen moves towards Ash's Pikachu, who starts running, powers up anElectro Ball, and then fires it—at a Throh in White—Victini and Zekrom, or a Sawk in Black—Victini and Reshiram. Pikachu then runs to Ash. The trio reaches a fork in the road; Cilan looks at his map and tells the group to go left in Black—Victini and Reshiram, or right in White—Victini and Zekrom.
In White—Victini and Zekrom, the screen then moves to a hot desert, where a man named Damon is traveling by foot. Damon comes upon a young Blitzle with an injured leg, and he calls upon hisReuniclus's Psychic to help him carry the injured Blitzle on his shoulder. Damon, Reuniclus, and Blitzle turn to walk back to a small village to find Blitzle's owner, a little girl named Luisa. Luisa's father thanks Damon for helping, but tells him to go home and that his plans are useless. Damon then tells the man that Eindoak Town can be revived, but he is again rebuffed.
At that moment, a dust storm appears in the desert, and heads towards the village. A herd of Bouffalant are startled by this, and they begin to stampede towards the village. Damon goes to check out the disaster and holds up his hand, cueing the appearance of Reshiram. Damon then climbs on Reshiram's back and orders it to destroy the dust storm, which it does with power and ease. Damon then asks the townspeople, who are shocked by the Legendary Pokémon's appearance, to give him another chance.
In Black—Victini and Reshiram, the scene instead shows Damon and his Gothitelle visiting a town on a frozen tundra. He discusses the matter of the Kingdom of the Vale's revival with a resident there, but is again dismissed. He refuses to leave, asking to see Glacine, the village's chief. She and her son Luis are on a cliff working to find herbs with his Lillipup's help. Below, on an ice shelf, a group ofBeartic become agitated when a giant iceberg collides with the ice. The cliff fractures, causing Luis to fall; then, as his mother and the first resident are trying to rescue him, the ice they are standing upon breaks off, stranding all of them in the path of the iceberg. Damon's Gothitelle saves Luis's Lillipup from falling into the water, and then Damon himself appears with Zekrom to destroy the iceberg. Damon and Zekrom reiterate their proposal, and, awed by the display, Glacine and her village reconsider.
Near Eindoak Town, Ash, Iris and Cilan find a pair of Deerling in danger on a cliff face. Ash attempts to rescue them but begins to fall himself; however, he is rescued when Victini touches his foot out of his sight, giving him the ability to jump hundreds of feet across the canyon. Now separated from his stunned friends, Ash agrees to meet Iris and Cilan later and heads into a cave with the two Deerling. Victini shows Ash visions of the path he should take, allowing him to find his way through the cave. He reaches a giant cavern with a mesh of crystal paths, and Ash's presence mysteriously activates an orb and the crystals, before he is guided again to the cellar of Eindoak Town's castle and up to its balcony. There, he reunites with his friends.
Cilan explains that the castle is known as the "Sword of the Vale", and is said in legend to have flown to its current location from a valley far away. While exploring the castle, Ash, Iris and Cilan share some macarons among themselves, but an invisible Victini keeps stealing Ash's macarons, much to his disbelief. The group hears fireworks outside, which causes Victini to choke on a macaron as the group realizes they must hurry to the town's battle tournament. In the ruckus, Ash runs into the invisible Victini—this confuses him for a moment, but he brushes it off. The group encounters a relatively plain-clothed Damon, who introduces himself as the castle's caretaker and offers to escort them to the town, which they accept.
In the town square, the group meets a woman named Juanita, who runs a Victini-themed souvenir stand with her Golurk (which is Shiny in Black—Victini and Reshiram). The town's mayor, Mannes, gives a speech to the townspeople congratulating them for the bountiful harvest they have collected. Mannes sends his KlinkKlang and Klinklang into a large music machine, starting the festival. He explains the tournament's rules: each competitor has been given a necklace and must challenge other competitors throughout the town, with losing Trainers surrendering their necklaces until the winner emerges.
In the first round of the tournament, Ash faces Mako and her Serperior, which he defeats with Pikachu's Electro Ball. Iris battles a Trainer named Tatsuki and his Emboar with her Emolga, but Emolga uses Volt Switch, forcing Excadrill to come out in its place, against the rules; the referee promptly awards the match to Tatsuki. Juanita's daughter, Carlita, and her Hydreigon (Shiny in White—Victini and Zekrom) quickly dispatches of Cilan's Pansage. Ash and Oshawott later battle Tatsuki and defeat Emboar with Aqua Jet.
Ash sends Tepig to face Leeku and his Samurott, and Samurott's Razor Shell effortlessly smashes Tepig into Juanita's stand of Victini trinkets. However, Victini covertly appears and powers up Tepig, allowing it to defeat Samurott with an absurdly powerful Ember. Carlita witnesses this, and, becoming suspicious, challenges Ash. When Ash's Scraggy attempts to Headbutt Hydreigon, it is knocked into the trees. Carlita sees Victini give Scraggy a powerup, after which Scraggy quickly defeats Hydreigon with a second Headbutt. Carlita surrenders her necklace to the judge, and then confronts Ash, informing the group of Victini's role.
Suspicious that Victini was the one who stole the macarons, Ash uses one to bait it out. It appears, and Ash excitedly tries to befriend it. Victini is initially receptive and playful, but becomes alarmed as Ash swings it around enthusiastically, leaving the Pokémon of the group to coax Victini back to them. As the party travels through town, Victini hesitates in the shadow of giant pillars. Ash tries to force Victini forward, but Victini gets clobbered by a magical barrier around the castle area, delineated by the pillars and preventing Victini's escape. Upset, Victini flees back towards the castle. Later, while looking for Victini with Juanita and Carlita, they run into Mannes and Damon. It is revealed that Damon is Juanita's son and Carlita's older brother. He has been traveling and has not contacted Juanita in some time, which she reprimands him for. Carlita attempts to cheer him by telling him about Victini's appearance, but he says he already knew.
At Mannes's home, Victini is found leading a group of other Pokémon. Inside, Mannes relays the legend of the tribe now known as the People of the Vale: one thousand years ago, they were a prosperous people who lived in a place called the Kingdom of the Vale, in a valley where the Sword of the Vale originally resided. They used a power in the earth called the Dragon Force to enrich their land, and all was well. However, one day, the twin sons of the king—the Hero of Truth, who controlled Reshiram, and the Hero of Ideals, who controlled Zekrom—began a war over their beliefs. Reshiram and Zekrom battled and drained each other's strength, and then turned into orbs called Dragon Stones. The kingdom was devastated, and the Dragon Force corrupted and chaotic, ravaging the earth instead of healing it. Desperate, the king asked Victini to lend him its power, and he created the Pillars of Protection and their barrier to control the flow of that power. Using this system, the king flew the Sword of the Vale, with all of the townspeople inside, out of the Kingdom of the Vale to a nearby mountaintop. There, the castle calmed the flow of the Dragon Force. However, soon after the castle landed, the king died, while the Pillars of Protection remained. The two regretful princes hid the Dragon Stones deep within the caverns of the Sword of the Vale.
While watching Ash and his friends play with Victini, Damon informs his mother that her dream—that the People of the Vale could one day live again in the Kingdom of the Vale, as relayed in a flashback—can now come true. He intends to borrow Victini's power just as the king did, and return the Sword of the Vale to its rightful place. Inside, without Ash and his friends, Damon relays his journeys over the past three years. Damon visited the scattered tribal settlements of the People of the Vale to try to find support for his dream to reclaim the land that was the Kingdom of the Vale. He was always rebuffed, until one day he heard a voice emanating from the chambers under the Sword of the Vale. He and Mannes investigated, walking on a crystal path when, inexplicably, the two found themselves separated onto different paths. Damon went on alone to find his Legendary dragon, and with it as his ally, he demonstrated the truth of the legend and his dragon's power by helping the leaders of the settlements. (Here, each version of the movie briefly shows Damon's dragon in the area from the opening of the other version—Zekrom assisting in the desert in Black—Victini and Reshiram, and Reshiram in the tundra in White—Victini and Zekrom.) The leaders agreed to help him—and as if on cue, they appear in Mannes's study in support of Damon's goal: the resurrection of the Kingdom of the Vale.
Victini dreams about its millennium trapped in the Pillars of Protection, witnessing the establishment and growth of Eindoak Town. The dream ends with the spirit of the king returning to apologize for the trap, then saying goodbye and fading away; Ash inexplicably experiences the dream as well, and is awoken. Victini takes Ash, Iris, and Cilan to a balcony, where it shows them the sunrise over an ocean shore; Ash comes to understand that Victini wishes to go to the shore, and promises to take it.
Meanwhile, at the Sword of the Vale, Juanita and Carlita watch as Damon prepares to execute his plan on the observation deck of the castle. He sends out his Sigilyph, and it takes its place in a mechanism atop the chamber. Sigilyph's power awakens the thousands of Solosis and Duosion in the lower chambers of the castle, and in turn, the Pillars of Protection activate, rise, and begin to travel towards the castle. Alarmed, Victini flees from the ever-constricting barrier, eventually flying to the castle, where Damon requests that it lend him its power. As Damon reminds Victini of the king, it is briefly cooperative until it gets caught in another, smaller barrier. The smaller pillars force it into a mechanism that begins draining Victini's power, using it to power up the Solosis and Duosion. As Ash, Iris, and Cilan arrive, the castle slowly ascends into the sky, and the healthy Dragon Force flows out, returning to the Kingdom of the Vale and beginning to restore it.
Ash, Iris, Cilan, Juanita, and Carlita rush into the main chamber and find Damon torturing Victini. Horrified that this was her son's plan, Juanita demands he stop, which shocks and upsets him. When Ash attempts to destroy the machine draining Victini's power, Damon attacks the group with his Reuniclus or Gothitelle. Damon's Reshiram or Zekrom then arrives, and Juanita attempts to fight the dragon with Golurk, but Golurk is defeated easily. Ash once again tries to climb the mechanism, but Damon's Psychic-type Pokémon knocks him out.
While unconscious, Ash receives a vision from Victini, of the king warning Victini to never let the Sword of the Vale be moved again, because if it is, the Dragon Force would return to run amok, causing a repeat of the disaster that struck the Kingdom of the Vale, and threatening the entire world. This has already begun, but with the castle now above the clouds, Damon and his dragon are unaware of it happening. Ash awakens in the cellar of the castle, and Juanita begs him to forgive Damon, as he truly believes he is doing the right thing. She then reveals that one thing can stop Damon's dragon: the other dragon, which should still be deep in the castle's dungeons, where had Ash passed through at the beginning of the film. As the group explores the crystal cavern, Ash and Pikachu soon find themselves suddenly separated, as Damon had been; Ash and Pikachu go on alone. A voice challenges Ash, and then the paths begin to collapse, forcing him to the bottom of the cavern. There, he finds the Dragon Stone, and hears a voice asking him for his ideal (White—Victini and Zekrom) or truth (Black—Victini and Reshiram). He answers that he wants to save Victini and fulfill his promise, satisfying the voice, which reveals itself to be Zekrom (in White—Victini and Zekrom) or Reshiram (in Black—Victini and Reshiram).
Mannes arrives, and meets Juanita, Carlita, Iris, and Cilan, having flown to the castle in a helicopter powered by his Klink, Klang, and Klinklang. He warns the group of the disaster on the surface, but by now they already know. Golurk returns to again fight Reshiram or Zekrom, but fails; however, the dragon's finishing blow is deflected by its opposite, which arrives with Ash riding on it. Ash jumps off at the courtyard of the castle, and then Zekrom and Reshiram engage in an epic battle in the sky. Inside the castle, Pikachu engages Reuniclus or Gothitelle.
Finally, Ash's dragon defeats Damon's, forcing it below the clouds, where they both witness the unfolding tragedy of the deadly Dragon Force. Pikachu defeats Reuniclus or Gothitelle and Ash climbs the mechanism, but Damon's dragon returns before he can destroy the barrier around Victini. Damon orders it to stop Ash, but it ignores him and instead destroys the mechanism to free Victini. Damon's dragon explains to him that it has heard the "land's anger", and then the two dragons blow away the clouds, revealing to Damon the devastation that the Dragon Force has caused. Panicking, Damon immediately becomes remorseful and begs Reshiram and Zekrom to help him stop the disaster. They agree, "lending their power" and redirecting some of the destructive Dragon Force into the Sword of the Vale—this powers up the Pokémon inside much more than Victini did, but also causes the mechanisms throughout the castle to become erratic, including the castle's flight.
Damon directs his family, Mannes, and Ash's group to leave immediately, fearing that the castle may crumble. Damon, meanwhile, insists that he will stay until the disaster is averted and the world is saved. However, when Ash tries to flee, the barrier generated by the Pillars of Protection continues to trap Victini inside, and Ash refuses to leave without it. Iris escapes with Carlita on Hydreigon's back, while Cilan and Juanita board Mannes's helicopter. As the pillars close in, the castle rocks, and Damon is thrown from it. Without warning, the Sword rapidly ascends into the sky, uncontrolled. All the Psychic-type Pokémon flee, leaving Ash, Pikachu, and Victini alone in the castle.
High in the Earth's atmosphere, the castle begins to frost over, and the thin, cold air begins to take a toll on Ash. Damon appears, saved by and now riding his mother's Golurk, while Reshiram and Zekrom attack the Pillars of Protection. But as the pillars are attacked, they are knocked towards each other, constricting even further around Victini. The pillars soon collide and close completely in the castle's courtyard, trapping Ash, Pikachu, and Victini within their walls. Damon tells Ash to hold on, as he is one of the dragons' chosen, and in a desperate bid to save them, Golurk fruitlessly tries to pry the pillars apart with its hands. Reshiram and Zekrom continue to destroy the pillars, but now several layers of pillars are in the way, and it proves too time-consuming. Inside the prison created by the Pillars of Protection, a weak and delirious Ash sadly apologizes to Victini for failing in his promise to take it to the ocean, before it becomes so cold that Ash's tears freeze and he falls unconscious.
Victini decides to use Searing Shot, which is too weak to break apart the pillars, but Ash is warmed and wakes up due to the attack. He witnesses Victini summoning up all of its power to activate V-create, its ultimate move. This finally destroys the Pillars of Protection once and for all, and the chaotic Dragon Force gets ejected into space—but Victini is nowhere to be seen. With the barrier and Dragon Force gone, Damon re-enters the castle and wraps Ash in a blanket that helps keep him alive.
Later, with Reshiram, Zekrom, and Golurk pushing the castle, Damon steers the castle down to the advancing tendril of the deadly Dragon Force. Just as Ash wakes up, he lands the Sword, calming the Dragon Force before it can destroy the entire planet. On the beach, Ash, Iris, and Cilan stare out at the ocean, saddened by the apparent death of Victini. Believing that Victini sacrificed itself to destroy the Pillars of Protection and save him, Ash apologizes again before flinging one of Cilan's macarons toward the ocean. However, the macaron suddenly stops in mid-air and is eaten—and Victini reveals itself to be very much alive, now freed from the barrier just as it always dreamed.
Damon falls to his knees, overwhelmed with guilt that his actions had backfired so badly. However, Juanita consoles him by telling him they will have a lot of work to do to rebuild the Kingdom of the Vale. Victini sends Ash a vision of it helping with the rebuilding, and he understands that their time together is at an end. Bidding farewell to Damon, Juanita, Carlita, Mannes, and the other People of the Vale, Ash, Iris, and Cilan depart for new adventures.
During the credits, Damon and Juanita lead the People of the Vale in their reconstruction efforts. A single sprout is seen on the once-dead land in the Kingdom of the Vale, implying that the area can indeed be revived. While traveling, Ash, Iris, and Cilan get caught in a windstorm created by Tornadus (in White—Victini and Zekrom) or a thunderstorm caused by Thundurus (in Black—Victini and Reshiram). They later travel through a town where the Team Rocket trio watches them from a café, with Peg passing by as well. Reshiram and Zekrom continue flying throughout the world, appearing in the skies in a variety of places.