The alarm sounds, though neither Goh or Ash are keen to get up for their first full day at the Cerise Laboratory. Mimey enters the room and wakes the boys up with his mime vacuum, before showing them to their breakfast, where they are greeted by Professor Cerise, his daughter Chloe, and Yamper. Chloe prepares Yamper's meal before leaving for school.
Later, Ash and Goh join Professor Cerise in his laboratory. Ren apologizes for being late, blaming the delay on his bus. Cerise's other assistant Chrysa reveals that a mass outbreak of Ivysaur is responsible for the chaos across Vermilion City. Professor Cerise hands Ash a smartphone and orders Goh to take his out before calling out a pair of Rotom. The Rotom enter Ash and Goh's smartphones, transforming the devices into Rotom Phones. Meanwhile, at the Team Rocket HQ, Giovanni orders Jessie, James, Meowth, and Wobbuffet to steal strong and rare Pokémon for the organization, and make Team Rocket known and feared across the world, promising to deliver them a new secret weapon meant to help them achieve these objectives.
Ash and Goh, meanwhile, spot Officer Jenny as she directs traffic around the traveling Ivysaur hordes. Goh takes the opportunity to scan the Ivysaur with his phone's Pokédex function, but he is left wondering why the Ivysaur are in the city. Officer Jenny admits that she cannot explain the Ivysaur, but reveals another problem – the Team Rocket trio. Goh reveals that he has heard of the Pokémon stealing organization, but questions the validity of the reported talking Meowth. Ash replies that most people would assume so, but he knows otherwise. Officer Jenny orders the boys to be on alert as the trio have been reportedly sighted in the Vermilion vicinity.
Nearby, the crashing sound of an Ivysaur attacking a wall attracts Goh and Ash’s attention. Ash steps forward to help it, but Goh grabs his wrist to stop him from intervening. Ash, however, rubbishes Goh’s sentiments and prepares to hoist the Ivysaur over the wall. Ivysaur instantly responds by tackling Ash to the ground, which Goh notes only proves his point. Ash disagrees, causing Goh to reconsider his friendship with Ash. Goh instead decides to investigate for himself, much to Ash's chagrin. The boys watch as Ivysaur changes its approach, using Vine Whip to hoist itself over the wall. Ash and Goh both leap into action, attempting to scale the brick wall to pursue Ivysaur. While Ash climbs up easily, Goh struggles to grip on. Atop the wall Ash spots a mysterious building, which his Rotom Phone reveals is a Gym currently under construction. Meanwhile, the Ivysaur continues on its way and Goh finally makes his way over the obstacle. A Sweet Scent fills the air, and Goh admits that it is a sign that Ivysaur will soon evolve.
Continuing to investigate, Ash and Goh spot other Ivysaur and some Bulbasaur all walking in the same direction; towards the Gym. Goh soon consults his Rotom Phone for information on the under-construction Gym, which reveals that the area was once a grassland where the wild Bulbasaur and Ivysaur would bask in the sun. As they arrive at the construction site, the Pokémon are clearly disappointed. However, the beaming sun overhead spurs the Grass Pokémon into action, and they scale the scaffolding with their Vine Whips. Goh tries to explain their actions, but decides to abandon his thoughts and follow Ash up to the building's top. Goh initially struggles to climb, but with the help of Ash, the pair soon reach the top. The Ivysaur's flower opens as it absorbs the sunlight and a Sweet Scent fills the air once again. To truly understand the phenomena, he suggests they become Ivysaur. Goh is stunned by the suggestion, but follows Ash’s example, which helps him to realize the pleasantness of sun baking and the passing breeze. The Ivysaur and Bulbasaur begin to glow, when a net captures and interrupts the mass-evolution phenomena.
Hoisting their catch up to their balloon, the Team Rocket trio proclaim their arrival with a motto recital. Goh is shocked to finally come face-to-face with the evil trio and begins taking snapshots to record the talking Meowth. Ash orders the Pokémon be returned, but Team Rocket are keen to make a clean getaway. Seeing this, Ash has Pikachu use Iron Tail to free the stolen Pokémon from the net. Determined to settle an old score, Jessie orders Meowth to land the balloon. As the Rocket trio prepare to take on Ash, a Pelipper drops a coin-slot vending machine in front of them, which they realize must be the secret weapon Giovanni had promised to them. Jessie and James shove Meowth headfirst into the coin slot, using his golden charm to activate the machine. With a turn of the crank, Jessie and James receive a pair of Rocket-branded Poké Balls. Jessie and James are impressed by the Boss’s choices as they call out a Gyarados and a Tyranitar, respectively, onto the field. Pikachu dodges Gyarados's Ice Fang and Tyranitar's Fire Fang. He replies with an Electroweb, but the attack fails to hold back an oncoming Hydro Pump and Dark Pulse combo. Pikachu sprints into action with Quick Attack, striking both of his opponents in the forehead. Gyarados lashes Pikachu with an Aqua Tail and Tyranitar's Stone Edge hits its mark.
Ash rushes to Pikachu's side while Goh stands there, unable to attack as he doesn't have any Pokémon. Jessie and James prepare to deal the final blow, but the Ivysaur step up and launch a combined Solar Beam onslaught. Ash thanks the Ivysaur for helping. As Tyranitar and Gyarados charge up a their Hyper Beam attacks, Ash and Pikachu step in front of the Ivysaur to protect them from the anticipated powerful attacks. Ash orders a Thunderbolt, which combats the oncoming Hyper Beams and sends Team Rocket blasting off. Experiencing Pikachu's power once again, the trio agrees to resume their original plan to steal Ash's Pikachu.
Goh and Ash return their attentions back to the Ivysaur as they evolve into Venusaur. The newly-evolved Venusaur promptly unleash pollen into the air, causing the buds across Vermilion City to bloom into flowers. The young Bulbasaur follow suit, all evolving into Ivysaur. Goh realizes that the former grassland’s notable wind is the reason why the Bulbasaur evolutionary line frequent the spot. The impressive phenomena leads Ash and Goh to conclude that Pokémon are awesome. Goh also admits that Ash and Pikachu are cool, but Ash doesn’t hear the compliment. The research fellows return to the Cerise Laboratory, where the Professor is impressed by the findings on Venusaur's pollen. Ash and Goh conclude the day was great, with Ash simply glad to have made friends with the Venusaur. On hearing about "friends", Goh asks Ash if he will be his friend. Ash admits that they are already friends. Yamper's bark interrupts, announcing Chloe’s return from school. The boys chuckle among themselves as Chloe explains that she is late because she had to clean up after all of the school's flowers bloomed at once. Cerise declares the "Ivysaur march" phenomena is no longer a mystery, while Ash and Goh look forward to their next adventure.