On the way to Oreburgh, Ash and his friends see Nurse Joy trying to help an injured Nuzleaf. Nuzleaf is too upset to accept her help, so Brock steps in to calm Nuzleaf down. With help from Bonsly, who Nuzleaf seems to think is a Grass-type Pokémon, Brock wins Nuzleaf's trust and treats its injuries. This Nuzleaf must be lost, since an old tree on the other side of the mountain is the only place in the area where Seedot, Nuzleaf, and Shiftry are found. Ash and his friends volunteer to get Nuzleaf back where it belongs.
Team Rocket spies on the scene and decides Nuzleaf would be a great prize for the Boss. They show up with Meowth dressed as a Shiftry, hoping to trick Nuzleaf into coming with them. Their ploy is foiled, so they grab Bonsly and Nuzleaf. Brock tries to stop them and ends up getting carried away by Team Rocket too! That's no problem for Brock—Team Rocket lowers their guard after he cooks them a delicious meal, and Brock escapes with Nuzleaf and Bonsly. During the break-out, Bonsly even evolves into Sudowoodo!
Next Brock has to cross a river, but Sudowoodo dislikes water so Brock puts it in its Poké Ball. The problem is that without Sudowoodo, Nuzleaf gets upset! Brock has no choice but to bring out Sudowoodo and encourage it to be brave. Then Team Rocket catches up with Brock. Croagunk does its best but can't hold them off forever, so Sudowoodo pitches in to help fight. When Ash and Dawn arrive on the scene, Brock even tells them he and Sudowoodo can handle Team Rocket themselves! A real Shiftry shows up looking for Nuzleaf, and once Team Rocket is sent packing, our heroes can rest easy knowing that Nuzleaf will soon be back home.
During the night, a giant tree is shown, where the Seedot evolutionary line live. A Seedot falls down a branch and kicks a Nuzleaf off. It continues sleeping, landing on a Vileplume, running off into the forest. The next morning, the Vileplume continues running, emitting pollen and causing the Nuzleaf to sneeze, making the Vileplume run faster and dislodging Nuzleaf. It wakes up and realizes it is not at the tree. It tries to find its way back, running and falling off a cliff.
Meanwhile, Ash and his friends continue on towards Oreburgh City, one giant mountain in the distance separating them from the city, but a Pokémon Center is at the foot of the mountain. Ash wants to keep going, but Dawn wants to rest at the Center. Bonsly cries, and as Brock is feeding him solid Pokémon food, everyone noticing how much Bonsly has grown. They notice a gust of wind nearby and rush to check it. A Nurse Joy tries to approach the Nuzleaf from earlier, but it attacks with Razor Leaf. Brock steps in to protect her, but his romantic advance results in another Poison Jab from Croagunk and being dragged. Nuzleaf attacks Ash and Dawn, but they avoid the attack as Dawn checks her Pokédex. Brock gets back up and mentions that Nuzleaf are generally afraid of humans, but he steps forward and hides his hands, approaching and getting down to eye level, keeping Nuzleaf calm. Brock pulls a leaf off a tree and blows on it like a whistle, calming Nuzleaf more. Brock hands it an Oran Berry, but it refuses. Brock brings out Bonsly and has it eat some of the Oran before offering it to Nuzleaf. Nuzleaf accepts it as Brock presents a whole plate full of Berries. Nurse Joy notices how Brock was able to calm the Pokémon as he uses a Super Potion on Nuzleaf's wound, healing it. Nurse Joy mentions that the thousand year old tree nearby houses the Seedot evolutionary family, the only area to spot the Seedot family in the vicinity. The group decides to take the Nuzleaf to the tree. Team Rocket watches nearby, wanting to steal Nuzleaf, Meowth visualizing another Boss fantasy about Giovanni having Nuzleaf.
As the group walks, Bonsly and Nuzleaf bond, as Nuzleaf believes Bonsly is also a Grass type. Meowth, disguised as a Shiftry, appears as well as a disguised Jessie and James. They say that "Shiftry" is also trying to find the tree and try to lure Nuzleaf over. However, Dawn checks her Pokédex and it identifies Meowth, which destroys the disguise, even more by Meowth's speech. Team Rocket removes the disguise and recites their motto. Their balloon comes up and they board, using a bazooka net to nab both Nuzleaf and Bonsly. Before they get away, Brock grabs the net as Ash calls out Staravia. Jessie's Seviper uses Haze to stop Staravia and Team Rocket gets away.
Team Rocket puts the Pokémon in a cage and bind Brock to a tree. Brock tries to find a way to get free as Team Rocket gets hungry, noting that the food they have is merely garnish, not a complete meal. Brock gets an idea and says that he can turn the food into a full meal. They release him and Brock makes a full course meal, Team Rocket diving in. They are so occupied by the food that Brock manages to slip away, taking the whole cage and darting away. When they get far enough, Brock has Bonsly try Double-Edge on the cage. He manages to bend a bar, but not enough, and Bonsly starts crying. Brock reassures his Pokémon and he tries again, this time breaking a bar and opening the cage. Bonsly dances happily but begins glowing as he evolves into Sudowoodo. Brock is happy as he salutes him.
Meanwhile, Ash and Dawn continue to search for Brock, Staravia not finding anything. As they continue searching, Brock continues on, wondering how he'll manage to find Ash and Dawn, with Nuzleaf riding on top of Sudowoodo. They see the tree and continue on while Team Rocket flies in their balloon trying to find Brock after he slipped away. Brock runs into a fast-moving river and decides to cross. Knowing Sudowoodo hates water, he recalls him, but Nuzleaf crashes to the ground and starts crying. Brock brings Sudowoodo back out and tells him that Nuzleaf needs him. They start crossing, taking it slowly. Sudowoodo almost slips at one point, but Brock catches him. Just as they reach the end, Brock takes Nuzleaf off Sudowoodo as Team Rocket arrives nearby. Sudowoodo is paralyzed by fear as Jessie sends out Seviper and Brock sends out Croagunk. Seviper uses Bite, but Croagunk takes it without blinking. Effortlessly, he uses Poison Jab to send Seviper back. Seviper rushes forward with Poison Tail, but Croagunk's Poison Sting stops it, also hitting the balloon and causing an explosion, creating black smoke that Ash and Dawn spot, running towards it. Seviper uses Wrap on Croagunk, but he still manages to use Brick Break. While Seviper continues to Wrap, Croagunk repeats Brick Break multiple times, eventually dislodging Seviper and knocking it out. Brock congratulates Croagunk, but then notices him sitting there unresponsive, knocked out, as well, in a double knockout!
Brock recalls Croagunk as James sends Carnivine to attack with Bullet Seed. Brock shields Nuzleaf as Sudowoodo watches. He snaps out of fear and jumps to shore, getting wet, but not noticing. Sudowoodo steps up and dodges Carnivine's Bite before hitting with Double-Edge. Carnivine uses Bullet Seed but Sudowoodo uses Mimic to counter with Bullet Seed. Ash and Dawn arrive, noticing that Bonsly evolved. Ash wants to step in and battle, but Brock declines in that Sudowoodo can handle its first battle since evolving. Carnivine fires another Bullet Seed, Sudowoodo blocking and charging forward with another Double-Edge. Carnivine bites Sudowoodo and pins it to the ground, but Sudowoodo uses Flail to throw Carnivine off. Carnivine tries another Bullet Seed, but Sudowoodo dodges and uses Mimic to fire Bullet Seed and knock out Carnivine.
Team Rocket sends out Dustox and Cacnea. Ash decides to send Pikachu in, but a gust of wind overcomes the field as a real Shiftry appears. Meowth tries to convince Shiftry that Ash and his friends are the bad guys and they slip away while Shiftry advances. However, Team Rocket gets back in their balloon, now with a Wobbuffet design, and grabs Nuzleaf with a mecha arm. Shiftry uses Razor Wind to pop the balloon and free Nuzleaf. Shiftry saves Nuzleaf from the fall with a gust of wind. Ash has Pikachu use Thunderbolt to take down the Wobballoon for good. Nuzleaf returns to the tree as Ash and his friends continue on to Oreburgh City.