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Seems the road to Olivine City is a bit longer than expected, as Ash and his friends stare upon a large desert badlands. They start to go and Ash suddenly gets caught in a hole, Pikachu getting caught by a net. Brock and Misty look up, and who shows up? Team Rocket. They say their motto but Brock and Misty just help Ash out. Well... looks like the usual, Ash calls out his Cyndaquil to make short work of this. James sends Weezing and Cyndaquil clings on it, about to use Flamethrower just up close. Weezing shakes Cyndaquil off and Cyndaquil lands on the ground, head first. When it gets up, a swelling grows on its nose, making it a bit weak. Team Rocket poke fun at Cyndaquil for a while and then James tells Weezing to use Sludge, Ash blocking the attack. Ash tells Cyndaquil to use Flamethrower again and after feeling somewhat self-conscious, Cyndaquil does so; however, Weezing uses SmokeScreen at the same time, causing a massive explosion that sends Team Rocket and Cyndaquil blasting off. Afterward, Ash tries to look for Cyndaquil but it seems not to work well. Brock suggests they go to the local Pokémon Center for any clues.

Meanwhile, Cyndaquil wakes up and finds that it's lost and just tries to find a way around. A Sentret spies on it and calls out, a Butterfree and Sandshrew start to spy on Cyndaquil as well. Soon Cyndaquil collapses and then the Butterfree hovers above it. A Dugtrio soon picks Cyndaquil up and starts to carry him off somewhere.

At the Pokémon Center, Joy tells the gang that there's a legend about a sanctuary place for Pokémon in this desert. More likely Cyndaquil is there. Ash heads out, Brock and Misty following; however, Joy didn't tell them where the sanctuary was.

Team Rocket start to complain about the mess they're in until they see Cyndaquil being carried off. The want to get it but Jessie and James don't want to go, so they just throw Meowth down. Meowth lands on his face and gets his nose hurt too, causing another Dugtrio to carry him off with Cyndaquil. Jessie and James try to get out of the balloon and end up falling down. They follow the two Dugtrio.

Ash seems to find nothing much out in the desert, but Pikachu spots a couple of Quagsire up upon a hill. The Pokémon start to walk away from them calmly and the gang takes a hunch and follows them.

Jessie and James see that Cyndaquil and Meowth are taken into a mesa, with a wall of Exeggutor in front of the entrance. The two Pokémon are passed onto an Exeggutor and then they are carried into an oasis inside the mesa. (looks like the one in Mewtwo Lives) The two Pokémon stare around for a while, seeing that other Pokémon are running around enjoying this place. The Exeggutor calls out and a Miltank comes out of a hole in a tree. The Miltank walks up to them, greets them and proceeds to her work. She places a hoof on Cyndaquil's swollen nose and her tail starts to glow along with her hoof and then Cyndaquil, the swell gone in an instant. She then does the same to Meowth and his nose injury goes away as well. Seeing that they aren't coming out, Jessie and James make a run for it to the entrance, but the Exeggutor use Hypnosis and lead them out far away.

The gang finds a mesa, which might be the one. They see Jessie and James walk by, but they just walk by. Brock takes a notice of the Exeggutor in the distance, a direct approach won't work. Brock uses Onix and they dig underground to the mesa.

Jessie and James suddenly slam into a stone monolithic object and snap out of it. Seeing that they are back to their balloon. They soon get angry now that they are in the middle of nowhere, but James suggest they go for a little ride over there.

The gang make it to a tunnel with a river, Brock pointing out they should follow the light. They reach the sanctuary and Ash finds Cyndaquil and calls out to him. Which proves to be a mistake, soon all the Pokémon within the Mesa get angry and groups of Beedrill, Pidgeotto and Krabby surround them. Ash decides the only way is to jump and he does so followed by Pikachu. They get to the surface but the Pokémon in the sanctuary won't let Cyndaquil go to Ash and vice versa. Soon enough Team Rocket interrupts their little dilemma and decide to take the Pokémon in the sanctuary. They send out everything they got and order them to attack but Meowth stops them, saying that he doesn't want any harm to Miltank. This makes all of Team Rocket's Pokémon actually stop and not obey Jessie and James. Finding this useless, Jessie and James call them back and decide to take Miltank by other force. James shoots out a net and captures Miltank. Meowth grabs onto the net as the net climbs and gets up there but Jessie and James restrain Meowth before he could do anything. Ash tells Cyndaquil to use Flamethrower to the max and it does so, only cutting the rope that held the net. Ash quickly sends out Bayleef to use Razor Leaf to cut the net so Miltank can get out, Miltank landing safely in the water. Ash finishes the Team by a jolt of Thunderbolt by Pikachu which sends them flying sky-high.

Ash is glad to see Cyndaquil again and that it's feeling much better. And soon the Pokémon in the sanctuary respect Ash and the gang as they promise they won't tell anyone about the sanctuary. They head out towards Olivine City saying their goodbyes.

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