Ash and his friends are out behind the local Pokémon Center, preparing for their next challenges: Ash is training for the Battle Palace, and May is training with Eevee for her upcoming Contest. May calls for a Shadow Ball, and Eevee shows off its new move. Meanwhile, Brock is bottle-feeding Bonsly as he and Max watch their friends train and comment on how excited they are. Now, Ash has his Pokémon practice their attacks. Donphan's Rollout smashes through a boulder. Corphish's Bubble Beam splits the flying rocks from the smashed boulder into smaller pieces. Swellow practices its Quick Attack, and Sceptile attempts a Bullet Seed, but fails. Sceptile is both astonished and angry at itself for still not being able to attack.
Sceptile continues to try and fail, and falls to its knees in despair. Ash's other Pokémon attempt to comfort it, as do Ash and Pikachu, but their attempts don't seem to have any effect. Sceptile suddenly gets up and runs off into the woods in anguish. Ash and Pikachu immediately run off after it, while the other Pokémon and humans are worried about Sceptile. Brock comments that maybe the best thing for Sceptile would be for it to have some time alone with Ash and reestablish their bond. Ahead, Sceptile continues to run on, blindly, then reaches a tree and begins beating its head against it. After several hits, it backs up in pain, and drops to its hands and knees in despair. Ash then catches up, and tries again to encourage Sceptile. However, both Sceptile and Pikachu quickly hear something approaching, and we then see a swarm of Beedrill emerge.
They dive down to attack, and Ash desperately has Pikachu Thunderbolt them. But as soon as the attack drives off a group of them, another group appears to take its place. There are far too many for Pikachu alone to deal with, so Ash turns to Sceptile and says they have to go. The group tries to flee, with the Beedrill in pursuit, but they find themselves cornered on the edge of a cliff. There is a raging river in front of them, and an angry swarm of Beedrill behind them. As the Beedrill approach, Sceptile steps in front of Ash. Sceptile cringes as it takes a barrage of attacks. Ash holds up Sceptile's Poké Ball to recall it, but before he can, the Beedrill knock Sceptile back into Ash, causing him to drop the Poké Ball, and causing the three of them to fall into the river. Ash grabs hold of a rock in the river and calls out for Pikachu and Sceptile. Sceptile is carried towards him, and Ash grabs its arm before it goes past. Just then, the river also carries Pikachu past, but neither Ash nor Sceptile can reach it! The river carries Pikachu off as Ash cries out to it, swearing to find it as soon as he can.
Meanwhile, Team Rocket hides under a box, also worried about the Beedrill. A swarm of them appear and dive for Team Rocket, who quickly withdraws inside their box. They gloat that they are safe now, as they seem protected, but just then, the Beedrill manage to puncture the box and tear it apart. Team Rocket flees in fear, with the swarm in pursuit. Back at the Pokémon Center, May, Max, and Brock are worried because Ash, Pikachu, and Sceptile still haven't returned. They hear a voice behind them, and are greeted by Scott, who wonders where Ash is. May tells Scott what happened, and this alarms him. He explains that this is the time when the local Kakuna normally evolve into Beedrill, and there are a lot of them in the area. Realizing Ash and the others may be in danger, they decide to go look for them. Presently, Ash and his injured Sceptile are walking along, with Ash supporting Sceptile. Ash says that they have to get back to the Pokémon Center to get Sceptile some help. Suddenly, Sceptile falters, and falls to its knees in pain. Ash realizes that Sceptile is hurt worse than he thought, and says that they should rest now. Sceptile shakes its head no, but Ash assures it that Pikachu will be okay, then advises they get some rest so they can continue.
Scott is now leading the others into the woods in search of their missing friends. He shows the others the Repel he brought along to keep the Beedrill away. Bonsly then sees something ahead, which turns out to be Sceptile's Poké Ball. The group looks down at the raging river below and fears the worst. Scott says they should follow the river, so they hurry off. Ahead, Ash has put together a meal for himself and Sceptile using some Berries from the area. Sceptile now lies down to go to sleep. Ash apologizes for this, since it would have been more comfortable in its Poké Ball, but that this is the best they can do. Ash then looks up at the moon and thinks about Pikachu, hoping he is okay. Somewhere downriver, a very weak Pikachu struggles ashore and collapses, lacking even the strength to remain standing. Heavy approaching footsteps can be heard. They turn out to be coming from a Venusaur, with an old man riding on it.
Elsewhere, Scott's group is still following the river when they see a column of smoke in the distance, presumably from a campfire. At this fire, the old man sits next to his Venusaur, mixing something in a bowl. He finishes, and tells Pikachu to drink it. It does, and it doesn't seem to like the taste. Just then, Scott and the others approach, and Scott greets the man. May and Max are happy to see Pikachu, and ask if it is okay. Pikachu semi-weakly responds, and the old man says that it will soon be fine. He then greets Scott and asks who his companions are. Scott then introduces them to one of the Frontier Brains, Palace Maven Spenser. Ash's friends are surprised to learn of his identity, and explain that this Pikachu belongs to their friend Ash, who is still missing. At first, they want to keep looking, but then May and Max's stomachs both growl, and they all realize how late it is and that it has been a while since they have eaten. Venusaur then extends a vine and offers them some fruit, and Spenser says that they should best eat first before continuing the search. Farther ahead, Ash is now talking in his sleep. Lying opposite him, Sceptile is still awake, watching him. Content that Ash is okay, Sceptile smiles and goes to sleep itself.
Back at the campsite, the group explains to Spenser as they eat about what has been happening with Ash and Sceptile, and about how since it evolved, Sceptile hasn't been able to use any attacks. Team Rocket overhears this from some nearby bushes. They conclude that since Sceptile cannot use attacks, this is the perfect chance for them to steal both Pikachu and Sceptile. May, Max, and Brock are now finished with their food, and thank Spenser. Spenser tells them a bit about himself and the healing medicines he makes. Pikachu, who had been asleep, now wakes up, and is fully healed. Brock, May, and Max are of course happy to see this, and this shows that Spenser's medicines do work. The old man stands up now, and says that since they have eaten and rested, they should now resume searching, as dawn begins to break over the land.
Meanwhile, Ash and Sceptile are now walking again, with Ash supporting his Pokémon as before. Ash calls out for Pikachu, but then trips over a rock, and falls flat because of Sceptile's added weight. Sceptile is concerned, but Ash says he's okay. Still, when Ash tries to get up, he finds that he has hurt his knee. Still, he gets up and continues to walk and support Sceptile, determined to get to the Pokémon Center and get them both healed. Before long, they come across a group of Kakuna that may be about to evolve. Ash says that they have to be quiet as they go through here so the Kakuna don't evolve and start attacking. They proceed forward, but suddenly, a swam of Beedrill catches up to them. Ash and Sceptile increase their pace, but they come across a dead end. Ash turns around and picks up a stick, ready to fight the Beedrill. However, one of the Beedrill hits Ash hard, knocking him back. The swarm closes in, and Sceptile steps in front of Ash. It tries to use Bullet Seed, but again fails. Ash calls out to Sceptile, but suddenly, Pikachu intervenes with a Thunderbolt, having been closely followed by May, Max, and Brock. Ash is happy to see them, but then, the Beedrill quickly turn on the new arrivals. A powder suddenly calms them down; it turns out to be Venusaur's Sweet Scent, as Venusaur, Spenser, and Scott have now arrived. Brock thanks Spenser, who turns to the swarm and asks them to leave, which they do. Brock and May now tell Ash who Spenser is. Ash thanks him, but suddenly two claws grab Pikachu and Sceptile.
Team Rocket gloat at their success, and Spenser demands to know who they are, so they go into their motto. Ash calls for a Thunderbolt, but it doesn't work. They gloat that since Pikachu's attacks will not work, and Sceptile cannot attack anyway, there is nothing Ash can do. Giving chase, Ash spots a dead tree, climbs it, and prepares to jump. He cringes from the pressure on his injured knee, but ignores it and jumps, managing to grab the arm that holds Sceptile, much to Team Rocket's surprise. Meowth works the controls, trying to shake Ash off, but he hangs on. Infuriated, Jessie sends out Dustox, who attacks Ash with Poison Sting. Ash yells in pain, but he still hangs on and yells about not letting Team Rocket get away with this, as Sceptile anxiously looks on. Jessie now tells Dustox to knock Ash away with Tackle, and it does, causing Ash to fall. Sceptile screams, as the blade on its right arm grows and energizes. With a shout, it successfully uses Leaf Blade to free itself and Pikachu. Pikachu quickly jumps onto its back, and Sceptile uses Quick Attack to catch up to Ash. In the same motion, Sceptile catches Ash and immediately fires a Bullet Seed to soften their landing. Sceptile sets Ash down, Pikachu gets off, and Ash congratulates Sceptile on its success. Sceptile then falters, as it is overcome by its injuries. Spenser now steps in, and sends out a Chansey, who uses Heal Bell. This heals Sceptile, who promptly reaches into a bush and picks out a new twig. Ash and friends are elated to see that Sceptile is finally all right.
However, Team Rocket refuse to give up that easily. They land their balloon and prepare for battle. Spenser interrupts and says that they should almost be thanked, since it was their interference that allowed Sceptile to regain its confidence. Jessie angrily cuts him off and calls for a Tackle from Dustox, as James calls for a Needle Arm. Ash calls for a Leaf Blade, and one strike is enough to send Cacnea and Dustox reeling, much to Jessie and James' surprise. Ash now calls for Bullet Seed, which sends them blasting off. Later, Scott tells Ash about the Battle Palace, and Ash officially challenges Spenser, who accepts. So now that Sceptile has regained its moves and confidence, Ash can focus on his upcoming battle with Spenser for the Spirit Symbol.