A Mudkip Mission (Japanese: 秘密の池！ミズゴロウがいっぱい！？Secret Pond! Full of Mizugorou!?) is the 25th episode of the Advanced Generation series, and the 299th episode of the Pokémon anime. It first aired in Japan on May 15, 2003 and in the United States on March 13, 2004.
As our heroes set out on their journey again, they encounter a waterfall. Brock ties a rope to a rock and, with Lotad's help, wraps it on a branch above the waterfall. After Brock helps everyone up the rope, they discover a lake filled with Mudkip. Brock notices a baby being washed away in the current and sends Lotad to help. Lotad gets caught as well and a larger Mudkip jumps in and saves them both. At this point an older man comes out, afraid that Ash and company are trying to steal the Mudkip. They explained what happened and are invited in for lunch.
The man explains that he takes care of and raises the Mudkip in the lake. He even shows them a baby Mudkip hatching out of an egg. He explains that while most Mudkip leave to explore the world, the larger one stayed to protect the babies. Throughout lunch, Team Rocket is debating whether or not to enter the lake area. They of course, do so, knocking over some cans that the caretaker had set up as sort of a security system. The man hears the noise and goes to inspect what is going on. Team Rocket destroys the dam so that the Mudkip are washed away and they can catch them easier. Brock uses his Pokémon to save the Mudkip. The larger Mudkip jumps in the water to rescue a baby that was being washed away, only to get caught in the current itself. It clings to a rock on the side of the water fall and finally agrees to let Brock rescue it.
Team Rocket arrives again, this time in a robot with scoops for hands, which they use to capture the baby Mudkip. Brock tells Lotad and Mudkip to use Water Gun at the base of the robot, which creates a mud pit and sinks Team Rocket. Pikachu then sends Team Rocket on their way. The show ends with the large Mudkip deciding to leave the lake with Brock.
While the group walk along a river, May announces that it is time for another installment of "May's expeditions". As May continues to hold her fingers to form a camera position, Max declares that he hopes they'll come across some new Pokémon. As they continue to walk, they came to a waterfall. Faced with a hard climb up the steep cliff, Brock sends out his Lotad. He ties a stone to a rope and throws it up into the air and then, Lotad uses Water Gun to propel it up to catch on a tree branch at the top. After checking the rope to make sure it is secure, Brock climbs up first and the others follows behind. When Brock reaches the top, May helps everyone up to the top. Ash asks how May beat them and she says she used her Silcoon to glide up, where Max remarks if she were a real reporter she wouldn't give away her secret.
Everyone examines their surroundings, so Max checks his PokéNav and he reveals that the river is split by an island hence the gentler flow. The group continues to explore the wilderness. Shortly after, Brock warns them that the ground will be muddy ahead. They step out of the fog and see lots of baby Mudkip playing in the lake. Ash scans them with his Pokédex. May isn’t too thrilled as she recalls her first encounter with a Mudkip left her soaked. Though she quickly changes her mind, remarking the Mudkip are adorable, and rushes out to catch one for herself. However, a bigger Mudkip emerges from the bushes and uses Water Gun to keep her away. May bemoans her luck with Water Pokémon. Just then, one of the baby Mudkip falls into the river during a play fight and is soon swept away by the current. Everyone notices its plight and Brock quickly orders his Lotad to save it. Lotad jumps into the water and soon reaches the Mudkip, but the current is too strong for him and pulls him along too. Brock begins running to intervene, though the big Mudkip manages to pull Lotad and the baby back to the shore. Brock goes to thank the Mudkip for its help, but it leaps back with an angry look. Brock assures the Mudkip of his good intentions and apologizes for May's actions. The others approach, but the Mudkip flees into the forest. Brock turns his attention to the young Mudkip and is pleased to see it is unharmed. Suddenly a peculiar man with Mudkip fin-like hairstyle, pops out of the bushes. Ash and May initially mistake the guy for a Mudkip monster, but they quickly realize he is human when he scolds them for attempting to steal the Mudkip. Max quickly settles the situation, and the baby Mudkip chirps also reassure the man that Brock actually saved the infant.
They go back to the man's house, whose real name is Old Man Swamp or Swampy for short, for some tea. Brock spots some Eggs in a glass case, and Swampy reveals that those are Mudkip Eggs. He explains that he raises the Mudkip from Eggs he receives from the Pokémon League to be the starter Pokémon for Trainers starting their journeys in the Hoenn region. Swampy adds that Professor Birch also catches and raises starter Pokémon. Max exclaims that it is like being a Pokémon Breeder, though Brock retorts that it is a little different. Upon hearing this, Swampy takes the group outside to witness some Mudkip hatch. A Mudkip emerges from its shell and immediately sprays May in the face with a Water Gun. Brock then informs Swampy that a large Mudkip helped saved one of Swampy’s hatchlings. Old Man Swamp expresses worry about the larger protective Mudkip, adding that it is actually a wild Pokémon and is too boisterous for a new Trainer and that soon it will be left alone when its friends go off to start their own Pokémon journeys with new Trainers.
Later, Team Rocket stumble across Swampy's property fence and are left confused by why it’s out in the middle of nowhere. James suggests the fence might be to protect something valuable. With the thought of treasure, Jessie and James call out Seviper and Cacnea respectively, to attack the fence. Seviper's Poison Tail proves useless. Cacnea, however, uses Needle Arm which knocks James directly into the fence and incidentally breaking it. Wobbuffet emerges from his Poké Ball, triggering one of Swampy’s wires in the process. The rattling cans alert Swampy to the trespassers and he rushes to confront them, with Ash and his friends following behind. Brock, however, is led away to the river as the Mudkip from earlier appears before him. Mudkip emerges from its hiding spot again, so Brock offers it some Pokémon food to befriend it. Brock is unsurprised by Mudkip hesitance, admitting that they had only just met.
Meanwhile, Swampy, Ash, Max and May reach the boundary fence and inspect the extensive damage. Cackling laughter attracts everyone's attentions to the culprits as the Rocket trio performs their motto. Old Man Swamp declares he knows that they're trying to the steal the Mudkip. Jessie and her teammates are thrilled to hear that there are Mudkip to be stolen and begin fantasizing about their big promotions. As May scolds Swampy for informing Team Rocket of the Mudkip, he retorts that he has never been able to keep a secret. Swampy then says that breaking down the nearby dam would wash all of the young Mudkip away, only to realize he has just revealed yet another secret. James promptly calls out Cacnea and orders it to use Needle Arm. However, Cacnea lashes James with the attack, sending him through the dam wall.
The escaping water catches Brock's attention. As a large wave heads directly for the Mudkip, Brock sends out his Forretress to keep the water at bay with Rapid Spin while he and Lotad take the Mudkip to higher ground. Brock soon spots a young Mudkip caught in the raging current, though the large Mudkip dives in to rescue it. Mudkip reaches the young one, but it is unable to swim to shore and the pair are sent over the waterfall. Mudkip manages to cling onto a rock, with the baby in its mouth, as the waterfall beats down on it. Brock quickly spots his rope from earlier, still tied t the tree and promptly leaps into the water. He urges Mudkip to grab his hand, and after some desperate pleas it outstretches its tail. Brock strains to reach though manages to pull the pair of Mudkip to safety, while everyone hoists Brock to the top. Swampy thanks Brock for another excellent rescue, but Brock again offers all the credit to Mudkip.
The crashes of felled trees alert everyone to Team Rocket, who are now operating their mechanized Mudkip maiden. The trio get to work scooping up all of the Mudkip with their mechas shovel hands. Brock suddenly remembers the area's loamy soil, so he calls for Lotad and Mudkip to use Water Gun on the ground. Team Rocket are confused by the tactic, but quickly realize that their mecha is sinking into the ground. Mudkip than tackles the robot's loot bag, which frees all of the captive Mudkip. Ash follow up by having Pikachu use Thunderbolt, sending Team Rocket blasting off. Afterwards, Old Man Swamp thanks them for saving the Mudkip and asks Brock to take wild Mudkip with him, to which Brock accepts. Mudkip also agrees and leaps into Brock's arms. Brock reassures Mudkip that they'll be a team, and Swampy is chuffed to see the beginnings of a new friendship.