Ash and Pikachu head to Sakuragi Institute, which have just opened in Vermilion City, Kanto, along with Professor Oak. In the laboratory, they hear about a Legendary Pokémon that appears in the Vermilion port, so they run there to have a battle. Meanwhile, a local boy named Go is sure he knows what this Legendary Pokémon is and is also heading to the port.
In the Morning, Ash and Pikachu are asleep, until the alarm clock was on. Pikachu wake up and went to turn off the alarm clock, buy Ash hit Pikachu by accident and throw the alarm clock, which is now broken. Pikachu try to wake Ash and electrocute him, but Ash is still sleeping. Delia came and wakes Ash up, telling he is going to Professor Oak's Laboratory. Ash wakes up and rushes to Professor Oak's laboratory with Pikachu. Ash meets up with Professor Oak, who tells Ash that a young professor is opening a new laboratory in Vermilion city. Oak invites Ash to its opening ceremony, which Ash is thrilled to join in on it. Delia and Mimey appears where she brought lunch for Ash and overhear their conversation, and decides to join in Vermilion city so she can check out the restaurants and shopping malls. As they are driving, Ash is excited to see some of the old Pokémon, such as Diglett and Butterfree. Oak comments Ash always a trainer who love Pokémon and ask him if he still planing to a become Pokémon Master, which Ash states that will become one together with his partner Pikachu.
As they arrive at the laboratory, Ash and Pikachu went on ahead, while Professor Oak park his car. Ash encounters a yellow Pokémon, which he never seen before. Ash tries to befriend the new Pokémon as he wanna to know where its from and what its name, but it evades Ash and attempts to back away from him. Ash grabs it and hug it, only for it to electrocute him instead. The new Pokémon take a liking to Pikachu which they quickly become friends. Koharu come home from school where she greets Yamper, but saw Ash got electrocuted and slightly walk away from him along with Yamper. Ash wakes up and see Professor Oak who told to hurry up to the open ceremony. Inside the Laboratory, Professor Sakuragi, thanks everyone for coming at the open ceremony and explains about history of Pokémon. The Pokémon are strange creatures that lives on this planet and appear all over the world, where they live together with humans and form special with each other. Sakuragi explains the Sakuragi Institute is here to discovers the many mysteries of Pokémon to understand more about them and to help make the world a better place.
Above the ceremony, Koharu is reading while she is happily looking at Yamper, who is sleeping. Koharu gets up and look at the window, who is upset that Go didn't show up because he was going to be here and Koharu bring him his school work. Koharu then got a message from Go saying that he is going to have a fateful encounter and will be late, which annoys Koharu knowing his messages is always like this. Somewhere in Vermilion city, Go check out the weather on his phone, as its show that cloud are appearing at any moment. At the Sakuragi Institute, the computer is detecting that a rare Pokémon will appear at Vermilion port. Ash hears about this and decides to head there, while the other people follow him to see if may be a Legendary Pokémon at the port. Ash runs up ahead, knowing that he is first, however, he and Pikachu are blocked by a sleeping Snorlax in the path.
Go is prepare for the Legendary Pokémon's arrival as he counts down, but show no results and stumble upon a Psyduck, which he's nervous by as it walk away. Go then spot where the cloud is at the Vermilion port. The Legendary Pokémon emerges from the clouds and reveal to be Lugia. Trainers then attempt to battle Lugia in a raid battle, only for them and their Pokémon to be blown away. Go rushes to the scene to meet Lugia. The Trainers and their Pokémon continue to attack, but Lugia easily subdue them. Ash and Pikachu arrive and challenge Lugia to a battle, which Lugia responds with a roar. Ash order Pikachu to use Thunderbolt, but did no damage to it and got blown away while Ash catches Pikachu. Lugia then flies away from the port while Ash and Pikachu chase after it. Go arrives and spotted Lugia, where he and Ash jumps on the exact same time, as they were shock to meet each other, as they are flying away on Lugia.
Ash helps Go get on top Lugia, while Go is amazed to be riding on Lugia. Go starts to gather information on how Luiga fly and its skin is very rough, but sates that its very warm as well. Lugia roars and then flies up where Ash and Go meet a flock of Fearow. Go states that they are flying the same height as Lugia and are strong flyers. Lugia dives down and uses Hydro Pump, to open the ocean a bit which amazes Ash and Go. Ash hears a voice saying "Here we go!" as they are heading into the water. Underwater, the boys sees a whole bunch of Pokémon, as they are greeted by Horsea, which cause them to smiles. However, they soon began to lack oxygen, luckily, Lugia rises to the surface, which allows them to breathe. Ash states that meeting all kinds of Pokémon is truly great, which amazes Go by his character and accepts Ash as his friend. After introducing themselves, Lugia flies down and the boys came across more Pokémon, where Lugia drops them off and flies away. The boys thank Lugia for their time with it and hope to meet it again.
Ash states that Pokémon are nice, Go agree as Lugia reminded him on how big the world is. Go explains that anyone can go anywhere they wanna be and meet all kinds of Pokémon they want to meet, which Ash colies that a person can meet any of them for sure, which make them chuckles. Go declares that it time to go back, however, they realizes they are in the middle of nowhere, which annoys Pikachu. After being exhausted from their long back, Ash and Go finally made it back at the Sakuragi Institute. Pikachu gets welcome by his friend Yamper, while Koharu meets Ash and Go, who tells the latter that he's late. Go tells Koharu that he and Ash had a encountered with Lugia while Koharu gives Go his schoolwork, which Go mutters that don't won't actually need it. As Koharu get annoys by his statement, Go change the subject by where Professor Sakuragi, which Koharu tells him her father is talking with Professor Oak, which Go is happy to hear that Oak is here, rushes to meet. Ash overhears Koharu about Professor Sakuragi is her father, but get barked by Yamper.
Inside the Laboratory, Professor Sakuragi thanks Ash and Go for the data they collect from Lugia. Ash states that Lugia had took liking them, as he explains he felt a jolt when lock eyes with Lugia. Go even mentions that Lugia lessen the impact for them with a Hydro Pump, and Ash tells that he heard a voice as Lugia were plunged in the water. Professor Sakuragi and Go are surprise to hear about this and Sakuragi offers Ash and Go to become research fellows to deepen the knowledge of Pokémon. Ash and Go accept the offer which Sakuragi is glad about them join. Ash and Go starts a rivalry knowing of will lose to the other, as Delia appears and states commuting from Pallet Town to Vermilion City will be tough. Sakuragi has a solution for the problem, as he show Ash and Go their dorm. The boys are excited about and Go call dibs on the top bed. However, Ash states that he wants to be one who the top bed and starts another bickering. Delia decides to leave Mimey to look after Ash which it accepts. When Delia and Professor Oak leaves, Delia tells Ash to eat properly and brush his teeth and asks Go to look after her son, which Go accepts while Ash is embarrassed by his mother as they bid her and Oak farewell.
Koharu came and asks her dad is he ready. Sakuragi replies to her to wait a bit longer as he wants to take care on one last for Ash and Go. At the Lab, Sakuragi summons a Charmander, Bulbasaur, and Squirtle, which Ash get adorable by them while Sakuragi tries to give Go one of them as his Starter Pokémon for him to become a trainer. However, Go states want to have Mew as his Starter, which Sakuragi is surprise about his comment. Ash tells Go that he is a interesting guy, while Go tells Ash is more interesting himself, which makes Ash think he won. As the boys have another argument, Sakuragi tells them that he will look forward to learn Mew's secrets as Ash and Go prepares their journey together.
- "Who's that Pokémon?:" Lugia (JP)
- At the beginning of the episode, a collection of Ash's previous Badges and trophies are shown in his room. They include:
- The Pokémon League Badge from the Indigo Conference.
- The Winner's Trophy from the Orange League.
- Ash's Badges from the Hoenn, Sinnoh, Unova, and Kalos regions.
- His Symbols from the Battle Frontier in Kanto.
- His Z-Power Ring with Pikashunium Z.
- His Championship Trophy from the Manalo Conference.
- The Manalo Conference exhibition match trophy.
- A Poké Doll.
- This makes the Johto arc the only leg of Ash's journey not represented in this display.
- The way the Trainers did Raid Battle against Lugia is a reference to the Raid Battle against it in Pokémon GO.