Putting the Air Back in Aerodactyl (Japanese: ポケモン研究者シゲルと復活のプテラ Pokémon Researcher Gary and Revival of Aerodactyl) is the 16th episode of Pokémon Chronicles.
Professor Oak is at the docks, searching for a souvenir for Delia. Tracey calls Oak, for the boat to the island they are going to is nearly here. Tracey notices Prof. Oak had brought a lot of stuff, but it is all for Oak's grandson, Gary, who is studying there. Apparently, Gary found something and asked Oak and Tracey to come to the island. A man drives the boat to the docks, introducing as Jared, who will take them to the island. Tracey, Oak and Jared drive off, but are watched by Cassidy and Butch, who have been sent by Dr. Namba to the island "those two fools" are going to. Jared informs Professor Oak his grandson is finishing the project as they speak. Tracey notices a school of Seaking and starts drawing it, while Oak remembers he had a Seaking, who swimmed against the current, reminding Oak he was similar to it. Jared believes this is more amazing, what they are about to see. After arriving to the island, the group hears something. In a moment, they run off from an Aerodactyl, who flies off.
Gary and a scientist arrive to pursue Aerodactyl. Gary notices the group has arrived and greets them, along with the scientist, Dora. However, they are all concerned about the Aerodactyl. Butch and Cassidy took a boat to the island, intending on stealing the Aerodactyl. Inside the research center, Tracey and Oak find replicas of Aerodatyl, Kaubto, Kabutops, Omanyte and Omastar, who are now living as fossils. Gary admits they are researching prehistoric Pokémon fossils, like the Amber Stone Gary acquired on his travels, or the fossilized Aerodactyl egg. They analyzed the items and confirmed they both came from an Aerodactyl. It is after they wanted to revive an Aerodactyl, using those items. However, Gary and Dora show the destroyed room, as when they revived Aerodactyl, it went rogue, damaged the equipment and escaped from the lab. Suddenly, a little girl arrives, seeing Professor Oak, seeing he is much older than she believed. Dora is annoyed, as her little sister, Crystal, is not in her room.
Oak sees they still have to take back Aerodactyl, else it could attack anyone. Crystal thinks she could help by summoning her friends. They come to a reef, where Crystal whistles, summoning some Lapras, as well as Farfetch'd and Pidgey, asking them to look for Aerodactyl. Oak is pleased, thinking Crystal will be a good trainer one day. Butch and Cassidy try to find Aerodactyl, who actually manages to find them. Butch and Cassidy are startled and get blown off. Aerodactyl flies off, but Butch and Cassidy are determined to catch it, nevertheless. As Tracey, Oak and Gary search, Gary is feeling down, thinking he is not a proper researcher, or else Aerodactyl wouldn't be on the loose. Tracey and Oak remind him he revived Aerodactyl. Gary thinks he couldn't predict that, but Tracey thinks his rival, Ash, wouldn't get down because of one mistake. Gary asks how Ash is doing and learns he won new badges and caught new Pokémon. Gary thinks he should've continued being a trainer rather than a researcher, but Oak thinks the journey has begun and made Professor Oak proud. A Farfetch'd appears and warns them of something.
Crystal, Jared and Dora are trying to find Aerodactyl and are warned by Farfetch'd. The two groups meet at the mountain, where Crystal found the fossilized egg. The find Aerodactyl, asleep and sneak upon it. Crystal, by mistake, trips over, waking Aerodactyl up. Tracey climbs up and holds onto Aerodactyl's leg, as Aerodactyl flies off. Crystal whistles, summoning the Farfetch'd, ordering them to go after Tracey. Tracey asks Aerodactyl to fly lower, alerting Aerodactyl Tracey is with it and tries to shake him off. Aerodactyl flies down, allowing Tracey to jump down somewhat safely, while Aerodactyl is captured into a net by Butch and Cassidy. Gary sends Umbreon, Cassidy sends Houndour, and Butch with Hitmontop. Umbreon dodges Houndour's Bite and hits it with Tackle. Hitmontop uses Rolling Kick, but misses Umbreon. Crystal sends Ivysaur, who tackles Houndour and uses Vine Whip on Hitmontop. Umbreon uses Quick Attack, hitting both Houndour and Hitmontop, while Ivysaur sends Team Rocket in air with Solar Beam. However, Aerodactyl uses Hyper Beam, blasting them off.
Aerodactyl is free and flies off, but not to the ocean. Gary suspects it does not want to leave the island, because it is afraid, for it was recently revived. Oak thinks Gary is correct, since it was startled when Tracey held its leg, regardless how powerful it is. Tracey believes Aerodactyl is even more frightened, when Team Rocket tried to catch it. To get Aerodactyl back, Oak plans on calming Aerodactyl down and befriending it. Gary thinks they have to feed it, giving Dora the idea of seeds they found near the fossil egg. They return to the lab, where Gary examines the data and finds what the seeds match to. Crystal recognizes the fruit and shows the group the tree it grows on. Ivysaur grabs the fruit, while Oak explains Tracey Aerodactyl will soon be hungry from all the flying about. Aerodactyl arrives to the tree and the group goes hiding. Gary goes to feed Aerodactyl, but Butch and Cassidy arrive back in a helicopter.
Aerodactyl flies off and tries to gust off the helicopter. Cassidy pulls a lever, extending a robotic arm, grappling Aerodactyl. Crystal sends Ivysaur, who uses Razor Leaf, but the attack is deflected. Cassidy and Butch fly off, so Gary sends Dodrio, who leaps onto the helicopter and uses Drill Peck on the vehicle. The helicopter is damaged and Butch and Cassidy blast off once again by being hit by Aerodactyl's Hyper Beam. The group is pleased, though, later, they sneak onto Aerodactyl, who is eating the fruit at the tree. Aerodactyl notices them and is startled, but Gary and Crystal, along with the Pokémon, try to persuade it they are not here as enemies. Gary wants Aerodactyl to be its friends, but Aerodactyl is not convinced. To calm it down, Gary presents Aerodactyl with the fruit. Aerodactyl sniffs it and chomps the fruit down in pleasure.
Later, while Crystal feeds Aerodactyl (who eats the fruit in one gulp), Oak and Tracey decide to return back to the lab. Gary hopes he will revive an Omanyte or a Kabuto soon. Professor Oak trusts Gary fully he'll do good in the research about prehistoric Pokémon. Crystal comes back, asking if Oak will return to the island one day. Oak promises to return one day, while Tracey gives Crystal a drawing of Ivysaur, pleasing her. Oak and Tracey take a boat back to the land, bidding farewell. As they watch Lapras, Oak tells Tracey Gary is already an important researcher of an interesting subject.
Tracey reads the title episode.