Professor Oak and Tracey are visiting the island where Gary is currently doing research. But not only are Butch and Cassidy tracking their movements, the Professor and Tracey encounter a raging Aerodactyl the minute they arrive on the island! The researchers on the island study ancient fossils, and Gary had the idea to use a piece of amber and a fossilized Egg to revive ancient Pokémon. However, as soon as they revived Aerodactyl from the Egg, it escaped and went on a rampage! Crystal, the little sister of head researcher Dara, asks all her Pokémon friends on the island to help look for Aerodactyl. Sure enough, one of the Farfetch'd sees Aerodactyl and leads everyone to the spot.
Aerodactyl is sleeping near the spot where the fossilized Egg was found, but it wakes up and flies off. Tracey tries to grab onto it, only managing to jump off after a wild ride. Then, before everyone's eyes, Butch and Cassidy snag Aerodactyl in a net—Team Rocket has come to the island to grab this ancient Pokémon! Gary's Umbreon and Crystal's Ivysaur are able to beat Team Rocket, but Aerodactyl frees itself and flies away, agitated. It seems overwhelmed by its new environment, so the researchers figure out what food it likes in the hopes of understanding Aerodactyl's behavior.
As predicted, they find Aerodactyl eating in a grove of fruit trees, only to have Butch and Cassidy show up yet again. This time, they use a helicopter to help capture Aerodactyl and carry it away. Crystal's Ivysaur tries to stop them, but Gary just has his Dodrio jump on the helicopter to wreck Team Rocket's plans and help free Aerodactyl. Once free, all Aerodactyl wants is to eat in peace, but Gary approaches it with a peace offering of fruit. That wins Aerodactyl over, and soon Aerodactyl is happily eating the food that Crystal offers, too. With everything on the island back to normal, Professor Oak and Tracey say their fond farewells and return to Pallet Town.
At a small town port, Professor Oak is looking at souvenirs and considering buying some for Delia. As he chooses between dark-chocolate Chansey and cream-filled Lickitung, Tracey calls him over to the pier. As Professor Oak sets down his suitcases, Tracey comments that he has packed a lot of stuff for the two days they will spend on Sayda Island. Professor Oak explains that they are presents for his grandson Gary. They wonder what Gary meant when he told them they had to see it, though Professor Oak is just looking forward to seeing him. Also destined for Sayda Island are Butch and Cassidy, on another mission ordered by Dr. Namba.
Just then, a boat arrives at the pier. Professor Oak and Tracey confirm who they are and the driver identifies himself as Jared, a research and development assistant at the Sayda Lab. The boat sets out, Jared tells Professor Oak and Tracey that Gary would have come to pick them up but he is finishing his project as they speak. Professor Oak asks what kind of project it is, though Jared says that he will see. A school of Seaking jumps out of the water exciting Tracey, as he has never sketched them before. As he makes his sketch, Professor Oak remembers having a Seaking when he was a Trainer after seeing it heading upstream near Vermilion City, as he felt that he could relate to it. As he concludes that they are pretty incredible, Jared tells him that Seaking aren't half as incredible as what they are about to see. As the boat arrives at Sayda Island, Jared tells Professor Oak that he won't believe what his grandson has done.
They walk along a path towards the lab until they hear a strange noise in the distance. Suddenly, an Aerodactyl appears in front of them. They fall to the ground and the Aerodactyl flies away. Just as Professor Oak shows his surprise at it being an Aerodactyl, Gary and head researcher Dora appear calling for it to come back. Gary forgets the Aerodactyl's escape to greet Professor Oak and Tracey. Professor Oak asks about the Aerodacty, but Gary says they will explain when they get to the lab. Meanwhile, another boat arrives on the beach; Butch and Cassidy jump out and start searching for the Aerodactyl.
Inside the lab, there is a large display with life-size reconstructions of all the Kanto Fossil Pokémon. While they are now extinct, their DNA can be studied through the Fossils they left behind, such as the Old Amber that Gary found while he was on his journey. Dora explains that they already had a fossilized Aerodactyl Egg at the lab before Gary arrived. When Gary found that the DNA matched, they got the idea to combine them to bring an Aerodactyl back to life. Gary tells his grandfather that congratulations aren't in order, and shows a lot of destroyed equipment thanks to newly revived Aerodactyl. Arriving on the scene, Dora’s little sister, Crystal, mentions that she was the one who actually found the Fossil Egg. Professor Oak says that they need to find the Aerodactyl since it could be dangerous if it crosses the ocean. Crystal says that her friends could help them out. She whistles to her friends, some Lapras and Farfetch'd, and asks them to find Aerodactyl. Professor Oak comments that she will make an excellent Trainer one day.
Up in a tree, Butch and Cassidy are surveying the area. They are ready to concentrate, but Aerodactyl then flies up in front of them. It uses Gust to send them into the bushes below.
As they prepare a bigger net, Gary, Tracey and Professor Oak walk along a path calling for Aerodactyl. They stop when Gary sadly says that he should never have become a researcher, as all he wanted to do was be the best and make Professor Oak proud. Professor Oak and Tracey are more positive as reviving an Aerodactyl is a great accomplishment. Gary says he should have realized the consequences, to which Oak replies that everyone learns from their mistakes. Tracey adds that Ash wouldn't get so discouraged. Gary then asks if they have heard from Ash, and is pleased to hear that Ash has already collected several Gym Badges in Hoenn. Professor Oak assures Gary that his new journey has just begun and Tracey adds that leanring is more important than the destination.
The Farfetch'd appears, gathering all the search party up at the islands highest point, where Crystal informs them that she found the fossilized Egg. Nearby, they find the Aerodactyl sleeping by a rock and try to sneak up on it. However, Crystal trips and disturbs it. The Aerodactyl flies off, though not before Tracey jumps and grabs onto one of its legs. As Tracey gets further away, Crystal calls to the Farfetch'd to follow. A scared Tracey asks the Aerodactyl to fly lower, alerting it to his presence and resulting in it trying to shake him off. As the others give pursuit, Aerodactyl flies over a clearing and Tracey jumps off.
While they check if Tracey is okay, a net suddenly appears and traps Aerodactyl. Butch and Cassidy announce their presence with a motto recital. As Cassidy declares that Aerodactyl is now theirs, Gary calls on his Umbreon. Cassidy sends out Houndour and Butch sends out Hitmontop. Houndour starts by using Bite on Umbreon. However, Umbreon dodges and counters with Tackle. Hitmontop then uses Rolling Kick which Umbreon also dodges. Crystal then tells Butch and Cassidy that they will pay for messing with Aerodactyl and sends out her Ivysaur. Ivysaur Tackles Houndour and then attacks Hitmontop with Vine Whip. Umbreon now uses a Quick Attack to send both Pokémon flying back. Ivysaur finishes with a Solar Beam that sends Butch and Cassidy into the air. From within its net, Aerodactyl uses a Hyper Beam to send them blasting off again.
This blast broke the net, allowing Aerodactyl to fly away again. It heads towards the ocean, but then turns around. Professor Oak guesses that it doesn't want to leave the island, which Gary agrees with realizing that it is because it is new to the world. Tracey wonders why such a powerful Pokémon would be scared of them. Professor Oak replies that a lot of Pokémon don't realize how powerful they are, and its confusion and the actions of Team Rocket have probably made it even more scared of humans. Professor Oak says that they now have to show that they don't mean it any harm. The question is how, and so Gary suggests feeding it. Dora then remembers that they found some fossilized seeds were discovered near the Egg.
Back at the lab, Gary compares the DNA of the seeds to the fruit DNA in their data bank. They find a match and Crystal recognizes that it still grows on the island. While Ivysaur picks the fruit, Professor Oak comments that all the flying will make it hungry soon. Aerodactyl soon arrive and is visibly enjoying the fruit on offer while the humans hide. Gary volunteers to feed it the one they have, but a helicopter appears in the sky.
Inside, Cassidy and Butch prepare another capture attempt. Aerodactyl flies off and the helicopter gives chase. As it reaches the ocean, Aerodactyl turns around and uses Whirlwind on the helicopter. Butch is finding it hard to keep control so Cassidy sends a mechanical arm forward to grab Aerodactyl. Crystal sends out Ivysaur to use Razor Leaf, but the attack doesn’t work on the helicopter’s metal construction. So Gary calls out his Dodrio, and it uses its powerful legs to leap onto the helicopter. It follows up with a fury of Drill Pecks which eventually cause the helicopter to blow up. A Hyper Beam from Aerodactyl sends Butch and Cassidy blasting off again. Crystal and Gary tell Ivysaur and Dodrio that they were great. Professor Oak comments that now they only need to get Aerodactyl to trust them.
As Aerodactyl eats another fruit, the group sneaks up on it again. It spots them and stands its ground, so Gary and Crystal run forward and try to convince Aerodactyl that they are friends with Pokémon. Umbreon, Dodrio, Ivysaur and the Farfetch'd come forward to confirm this. Gary tells it that they trust and care for each other and that they want to be its friend. Aerodactyl stops to consider this but then stands its ground again. Professor Oak is now unsure about the plan, but Gary walks forward to offer the fruit to Aerodactyl. Though Aerodactyl is scared, Gary manages to get it to eat the fruit. This makes it happy and it now becomes friendly towards them.
By the boat, Professor Oak and Tracey are getting ready to leave. Gary says he wants to research extinct Pokémon and Dora adds that they are offering him a job. Professor Oak tells his grandson that whatever he will do, he will do it well. Crystal comes over and asks if the Professor will come back. Oak assures her that he will and Tracey gives Crystal sketch of Ivysaur, which she loves. As everyone waves goodbye, Professor Oak tells Crystal to look after Aerodactyl and she tells him that he is the coolest. As the boat travels across the ocean, Tracey points out the Lapras to Professor Oak. Tracey says that Gary will be a great Pokémon Researcher, but Professor Oak corrects him; saying that he already is.