We see Professor Oak shopping for gifts in a store. Tracey calls for Professor Oak to come on over. Tracey notices that Professor Oak has packed a lot of stuff and he just tells him that they are mostly presents for Gary. A boat comes and picks them up. The boat driver introduces himself as Jared and they head off to Gary's lab. Cassidy and Butch watch them go and they plan to take something...
On their way to the lab, Jared tells them about what Gary is doing. Professor Oak sees a school of Seaking and Tracey decides to sketch them in his notebook. Professor Oak tells a story about his Seaking and how he found it. They arrive at the island. While walking to the lab, they hear a strange sound coming from the trees. Suddenly, an Aerodactyl flies out. Professor Oak, Tracey, and Jared duck for cover and the Aerodactyl flies away.
Gary and his assistant come running by. Gary says hi to the group and his assistant introduces herself as Dora. Gary decides to tell them about the Aerodactyl once they get back to the lab. Meanwhile, Cassidy and Butch have arrived on the island and they decide to capture the Aerodactyl.
At the lab, Professor Oak and Tracey see a display of the prehistoric Pokémon. Gary says that he found Old Amber on his journey. They continue walking and Gary tells Professor Oak that he is reviving extinct Pokémon. The Professor is very impressed by this. Gary leads them to another room and Tracey and the Professor are shocked to see that it's destroyed. Gary tells them that he and Dora revived the Aerodactyl in that room. Gary tells his story on how they revived it and what happened to the room.
Suddenly, a little girl pops out. The little girl's name is Crystal who happens to be Dora's sister. She claims to have found the fossil egg herself and she also knows a lot about Pokémon. Professor Oak tells them that they have to find Aerodactyl. Crystal tells him that she will get her best friends to help. So Crystal tells Lapras and Farfetch'd to help find Aerodactyl. Cassidy and Butch are on a tree looking for Aerodactyl. Aerodactyl comes and it knocks Cassidy and Butch off their tree and onto the ground and then it flies away.
Professor Oak, Gary, and Tracey continue to look for Aerodactyl. Gary feels a bit down because of the escaped Aerodactyl. Professor Oak tries to cheer Gary up and Tracey tells Gary that Ash wouldn't give up. Gary asks how Ash is doing and Professor Oak tells him that Ash is in the Hoenn Region collecting badges. Farfetch'd comes down and tells them that it has found Aerodactyl. Crystal, Dora, and Jared are also looking for Aerodactyl. Farfetch'd comes down to them and it tells them to follow it. The group meets up again and they see the Aerodactyl sleeping. They walk a bit closer to the Aerodactyl when Crystal falls and makes a loud noise. The Aerodactyl wakes up and begins to fly away but Tracey grabs hold of the Aerodactyl's leg and flies away with it. Aerodactyl doesn't even know that Tracey is on its leg. Crystal tells Farfetch'd to follow Tracey. Tracey talks to Aerodactyl and Aerodactyl freaks out like it's scared of Tracey. Tracey jumps off the flying Pokémon and lands hard on the ground.
Suddenly, a net pops out and lands on Aerodactyl. Aerodactyl falls on the ground and Team Rocket comes out to say their motto. Gary sends out his Umbreon and then Cassidy sends out her Houndour and Butch sends out his Hitmontop. Houndour uses Bite on Umbreon but Umbreon dodges it and uses Tackle. Hitmontop uses Rolling Kick but Umbreon dodges the attack. Crystal sends out her Ivysaur and it uses Tackle on Houndour. Then Ivysaur uses Vine Whip on Hitmontop. Gary commands Umbreon to use Quick Attack. Both Houndour and Hitmontop fall to the ground. Finally, Ivysaur uses Solarbeam and Aerodactyl uses Hyper Beam which blasts them off. Aerodactyl flies towards the ocean but then turns around and flies to somewhere else.
The group continues to search for Aerodactyl. Tracey thinks that Aerodactyl is just scared and both Gary and Professor Oak agree. That must explain why it freaked out when Tracey was holding its leg. Professor Oak thinks that they need to find a way to calm the Aerodactyl down. They get an idea of trying to feed it and everyone else agrees that they should try to do that. They decide to try to find the food that Aerodactyl eats through the seeds.
Back at the lab, they examine the seeds and they find a match. Crystal tells them that she saw the fruit before and she leads them to the place. Ivysaur takes down a piece of the fruit with its vines. Soon, Aerodactyl comes and everyone else hides. Aerodactyl happily eats the fruit and Gary decides to give it a piece of the fruit.
Suddenly, a helicopter appears from the sky. In the helicopter is Team Rocket. Aerodactyl flies away and Team Rocket goes after it. Aerodactyl slows down and it uses a Whirlwind attack on Team Rocket. Team Rocket doesn't give up and Cassidy fires a mechanical arm at Aerodactyl to capture it. Crystal gets out her Ivysaur again and she tells it to use Razor Leaf. However, the leaves have no effect on the helicopter. Aerodactyl struggles but the mechanical arm doesn't give in. Team Rocket then heads back to Professor Nanba's lab. Gary sends out his Dodrio and he tells it to jump on top of the helicopter. Then the Dodrio furiously uses Drill Peck on the helicopter which destroys a part of it. Lastly, Aerodactyl uses another Hyper Beam which totally destroys the helicopter and it blasts off Team Rocket once again.
Aerodactyl starts to eat the fruit again and the group continues to walk closely to it. Aerodactyl notices them and gets startled. Gary and Crystal talk to Aerodactyl and they tell it that they're friends with Pokémon. Aerodactyl just stares at them. Still not trusting them, Aerodactyl ignores them and continues eating. Then Gary takes out a piece of fruit out of his pocket and he shows the fruit to Aerodactyl. Aerodactyl sniffs the fruit and eats it. Aerodactyl now trusts them.
Crystal holds out a plate of fruit for Aerodactyl and Aerodactyl gobbles it up in one bite. It's now time for Professor Oak and Tracey to leave and they all say good bye to them. Gary tells Professor Oak that he wants to study extinct Pokémon and Professor Oak seems to be very proud of him. Crystal comes by and says good bye to them. Tracey then gives Crystal a drawing of an Ivysaur and she tells him that she loves it. So they get back on the boat and they are off. On the ride they see a couple of Lapras swimming by and Professor Oak tells Tracey that Gary will do just fine in his research.