At Vaniville Town, the gigantic blue deer and enormous red bird clash against one another ferociously, and destroy every building that they come into contact with. The town's residents and their Pokemon are stunned by the sudden appearance of the two mysterious creatures, and scream with horror as they flee from their collapsing homes.

Y bangs hardly on X's window, and urges him to come out immediately. X feels his entire room shake as he remains in his curled up position, and thinks that Y is unusually violent today. He worries that she will tear down his house if she keeps on rampaging like that, and reluctantly makes his way over to his window. However, when he lifts a corner of his curtain to peek outside, what he sees astonishes him. The two combating creatures have apparently moved closer to the center of town, and are barely two blocks away from X's house. Before he could recover from his shock, X catches sight of Alexa and Viola as well, the latter fervently taking snapshots of the current situation.

X cringes at the presence of reporters and starts to withdraw, but Y bangs on the window to stop him. She states that something serious has happened, and X has already seen what needs to be seen. She urges X to leave his house now, but X refuses. The girl angrily demands to know why, and X gestures towards Alexa and Viola, stating that Y should know better than anyone that he has trouble dealing with the paparazzi and shady adults.

Outside the gates of X's house, Viola takes another snapshot, and Alexa wants to know if she has managed to get the creatures on picture. Viola replies that she has, and asks her sister if the beings are Pokemon. Alexa states that she has no idea, but recalls what she learnt from a story she did on a tale of Kalos that took place 3000 years ago. According to the tale, there are two legendary Pokemon who appear every 1000 years, and if her assumption is correct, the blue deer with jeweled antlers is called Xerneas, while the red and black bird with a long tail is named Yveltal.

Trevor clutches the three boxes containing the starters and Pokedexes tightly in front of his chest, and cries out in horror as he flees from the clashing Xerneas and Yveltal. His cry catches the attention of Y, and she quickly whistles to her Rhyhorn. The burly rhinoceros instantly leaps out from the front yard of the Garbena residence, and runs towards Y as the girl hovers towards it. Y skillfully somersaults onto its back before urging Tierno and Shauna to get on, and the three begin rushing to Trevor's rescue. However, just before they reach the orange-haired boy, Yveltal unleashes a glaring red beam from its huge wings, which strikes the ground in front of Xerneas and causes an explosion. Trevor is thrown into midair, and Shauna screams in horror as her friend falls. Fortunately, Rhyhorn propels itself off the ground by its powerful hindlegs to gain height, and Tierno manages to catch Trevor by his collar just in time.

Yet, one of the transparent boxes containing a starter and Pokedex falls from Trevor's grip, and in that instant, another explosion occurs, which further levels the area and forces the young trainers to cling onto Rhyhorn to avoid being thrown off. More buildings start to collapse from the blow, and Tierno watches in dread as his beloved Dancing School is turned completely into rubbles. At the same time, Shauna's Furfrou gets hurled into the air, and Shauna widens her eyes in terror as it goes out of sight. Y tells Rhyhorn to bring everyone to safety, and pulls her helmet back on. Trevor asks with a startled tone where she is going, and Y states that she must go back to X to get him out. Without another word, she leaves her three friends to Rhyhorn, and goes airborne with Fletchy.

On a hill nearby, a mysterious gang of people known as Team Flare stand to watch the fight between Xerneas and Yveltal. They consist of men and women who wear bright red suits with red shades, and each one has a flame-shaped hairdo that is of the same fiery red. They are led by three Scientists: a near-bald pale skinned man named Xerosic, who owns a Malamar and is the second in command of the organization; a woman with short purple hair named Celosia who has a Manectric; and another woman with shoulder-length green hair named Bryony who is accompanied by a Liepard.

Xerosic wears an expressionless face, and states that the creatures in front of their eyes are the legendary Pokemon whose power they seek. Unfortunately, given the current situation, it is clearly beyond their capacity to take control of the Pokemon. Celosia agrees that it is a pity, since they are only barely able to shackle one of them, and it is certainly impossible to handle Xerneas and Yveltal at the same time. Xerosic remarks that in order to give power to Team Flare's ultimate weapon, they will need to obtain the energy of the legendary Pokemon, and he truly thought this would be a good opportunity to do so until both beings appeared simultaneously. Celosia turns to ask one of her Grunts how team B is doing, and she is informed that they are currently heading towards the home of the possessor. Bryony is slightly worried that the situation in town is going to make things complicated, since their target, the Mega Ring, particularly its embedded Key Stone, cannot unleash its true power if it gets even slightly damaged.

Meanwhile, outside X's home, several other Team Flare members have gathered. A male Grunt cries that he has trouble breaking into the house, and reports his frustration to his leaders, who are two other Scientists of the organization: a woman with very short orange hair named Aliana; and another woman named Mable whose blue hair is tied up in loops. Together, they make up the team B Celosia talked about.

With Xerneas and Yveltal edging closer by the minute, it is only a matter of time before they demolish everything, including the house of the Mega Ring's possessor. Mable blames Team A's failure in securing their part as the cause of their current situation, and Aliana giggles that she should not get herself upset. She states that they shall be the ones to bring upon destruction before the legendary Pokemon do, and beckons to her female Pyroar, who immediately unleashes a blast of flames from its mouth towards the front door.

When Y arrives at the scene, she is appalled to see X's home burning up. She spots that X has been dragged out onto his front yard, and is cornered against the wall by the red suited people. She swoops down to land between X and the Team Flare Scientists, and asks if X is alright while questioning who the intruders are.

Mable is astonished by Y's sudden appearance, and Aliana giggles that she must be good friends with the possessor. Mable grunts that she will not allow anyone to get in the way, and orders her Houndoom forward. The devil hound clamps its fangs around Y's wrist, and hoists her off the ground by the arm before ramming her against the wall. It then opens its mouth, ready to unleash a Flamethrower, and X cries out in terror. At that moment, something punches Houndoom hard on the face, knocking it onto the floor, and X gasps in realization that Kanga has come to their rescue.

Aliana laughs that they do not mind taking on more opponents, and orders another Flamethrower from her Pyroar. Kanga turns its back to shield X and Y from the attack, and winces in agony as the flames burn harshly on its skin. Houndoom gets back on its feet to add its own flame assault, and the combined fire attacks begin to push the Kangaskhan to its limits.

X trembles with shock and disbelief as he watches his Pokemon suffer for him, and reaches out a hand to touch its face. His action reveals the mysterious bracelet on his left wrist, and Mable exclaims that the Mega Ring has finally been spotted. Aliana promptly orders Pyroar to claim it, and the lioness pounces X onto the ground before starting to drag him across the grass by yanking at the back of his collar. Y watches helplessly as X struggles to fight for air from the restraint around his neck, but is barely able to move since her body is still stunned by the previous injury.

Li'l Kanga the baby Kangaskhan peeks out from Kanga's pouch, and sees that both its mother and trainer are suffering tremendously. Rage quickly fills its head as it clutches its fists, and in that instant, something mysterious happens. The gem on X's Mega Ring starts to glow brilliantly with seven colors, and Li'l Kanga is soon enveloped by the same light. It then emerges with an altered appearance, which sports bigger eyes and a bulker body just like an adult Kangaskhan.

Everyone is bewildered by what has happened, and Li'l Kanga gives no time for its enemies to react. It charges towards Houndoom and Pyroar, and grabs them by their tail and mane respectively. It then whisks them around like iron balls on a chain, before hurling them off into the distance. Mable and Aliana are utterly speechless at what the baby Kangaskhan has done, and astonished that its change has given it so much power. Mable grunts that this is totally out of their expectation, and fumes that they did not prepare for this. Aliana calms her down, and suggests they retreat for now as they no longer have Pokemon to fight with. Left with no choice, Mable agrees and announces the departure of team B.

Back on team A's side, Xerosic makes contact with his boss, and reports that Xerneas and Yveltal have stopped their clash and are beginning to part from each other. The person on the other side of the call acknowledges it, and states that as long as the two are still in each other's presence, they would continue to fight and end up having an endless war. Xerosic wonders what they should do, and his boss says it remains a fact that their ultimate weapon will require an energy source, which means they have to gain possession of the legendary Pokemon someday.

Later, after Xerneas and Yveltal have departed from Vaniville, Trevor, Tierno and Shauna sit among the rubbles and keep their heads hanging low, neither saying a word as a million thoughts go through their heads. Soon, Y returns to the scene, and Tierno sees that she has brought along Kanga and X, whom she is dragging by the collar. Y notices the tears welling up in Shauna's eyes, and wonders what is wrong. The girl sobs that she has lost her Furfrou, and says it got blown away during the gigantic Pokemon's battle. Trevor reveals that the transparent box he dropped contained one of the three sets of starters and Pokedexes he received from Prof. Sycamore, and remarks that his Holo Caster has also been damaged. Tierno sighs that everyone has lost something important, and before Y could ask, he gestures towards the now demolished Dancing School, which causes the girl to cover her mouth in shock.

Tierno wants to know what they should do from now on, and Shauna states that she plans to go in search of Furfrou. Trevor voices out his desire to report the situation to Prof. Sycamore directly since he has lost the means to communicate with him, although he has managed to send off a clip of the two giant Pokemon via the Holo Caster before it was damaged. He believes that the professor may know something about them, and Y agrees that it is highly possible. She personally wishes to find out more about the people in red suits who attacked X, and Trevor thinks they should all travel together. Tierno asks Shauna's opinion, and the girl rubs a tear off her eye before stating that it is the only logical thing to do since they have been a gang of five since childhood.

Y then turns to X, and says he cannot pretend not to hear it because the ring on his wrist is what the enemy was after, making him a key figure in all of this. She points out that he really has no choice but to come along since his house has been destroyed and his comfort zone is gone. X puts on a frown upon hearing that, but remains silent as he curls himself up in a seated position. Y gets annoyed, and hollers that he has spent enough time in his pajamas. Without warning, she rips them off him, leaving him in his underwear, and the sudden chill causes the boy to take a big sneeze. Shauna, Trevor and Tierno laugh as Y throws an outfit on X, and Kanga also wears a grin while Li'l Kanga, who has returned to its usual form, steals another glance at its trainer before slipping back into its mother's pouch.

Later, Y has also changed out of her flying suit, and plops X onto her Rhyhorn since she knows the boy will not voluntarily walk on his own. Trevor pulls on his bagpack, and muses to himself that life certainly takes unexpected turns. Daily routines that have remained the same for years could suddenly change without warning. Yet, what never changes is the strong bond between friends and Pokemon. Standing at the gates of Vaniville, Trevor will forever remember this day that he set out from his hometown with his childhood companions…