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.
Ash and his friends are walking along a river. May uses her fingers to form a camera position, talking to the "audience" as if she was on a nature TV show. As they continue to walk, they came to a waterfall. Faced with a hard climb up the mountain, 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 gang follows behind. When Brock reaches the top, May helps Brock, Ash, and Max up the cliff. 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.
Ash notices a foggy lake when Max checks his PokéNav he finds that the lake surrounds a small island. They decide to go there. 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 remembers an incident where a Mudkip used Water Gun on her. May rushes up while saying that she will catch one, but a bigger Mudkip came out of 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 lake and is washed away by the current. Everyone notices its plight and Brock quickly orders his Lotad to save it. Lotad jumps into the water and reaches the Mudkip, but the current is too strong for him and pulls him along too. Brock calls for it as the big Mudkip jumps into the water. It pulls Lotad and the baby back to the shore and Brock thanks it. The Mudkip leaps back with an angry look. Brock tells the Mudkip that May means no harm. The others approach but the Mudkip runs away. Brock picks up the baby Mudkip and plays with it. An old man with a Mudkip's fin-like hairstyle, pops up, scolding them for what they are doing with the Mudkip. Ash says that they mean no harm and told the man that Brock is the one who saved the Mudkip.
They go back to the Old Man's house, whose real name is Old Man Swamp, where they are allowed to see the Mudkip Eggs that the man is raising to go be starter Pokémon for Trainers starting their journeys in the Hoenn region. He expresses worry about the larger protective Mudkip due to the fact that it is too old and 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. However, Team Rocket has been secretly spying on the group. Making their move to try to steal the rare Mudkip with their newest mechas, they break down the dam and flood the river. Brock sends out his Forretress to keep the water at bay while he takes the Mudkip to higher ground. Team Rocket uses another mecha to scoop up the remaining Mudkip. Brock remembers himself saying how soft the ground is, and tells the Mudkip to use Water Gun, sinking the robot and rescuing the Mudkip. Then to send Jessie, James, and Meowth Blasting off, Pikachu uses a huge astral blast of Thunderbolt to destroy the mecha. Old Man Swamp thanks them for saving the Mudkip and asks Brock to take Mudkip with him, to which Brock accepts and the group walks off to the next town.