Ash and friends admire the nice Johto scenery when they spot a Houndoom delivering something. At the same time, Team Rocket is also admiring the scenery from the Meowth Balloon. Team Rocket spots Ash and his friends, so they interrupt them with their usual lines. James sends out Weezing and tells it to use SmokeScreen, making it impossible for Ash and friends to see. Jessie then tells her Arbok to attack Pikachu, but Pikachu is ready and fends it off with a Thunderbolt. With all the action, Togepi gets away from Misty and ends up near Weezing, so to get away it uses Metronome, which ends up Teleporting it far away. Team Rocket eventually loses to Ash as he sent out Chikorita to cut a hole through their balloon with its Razor Leaf and they were sent blasting off again.
The same Houndoom from before hears Togepi's crying and rescues it from atop a big tree. Houndoom sees that it is still sad, and gets an apple for it. A Pinsir then tries to attack Togepi, but Houndoom scares it off with its attacks. Houndoom tries to leave Togepi again, but hears its crying and comes back again. This time Houndoom puts Togepi on its back and continues on with its new friend.
Ash and friends at the same time are searching for Togepi. They all think of the worst, but then Ash has the idea of getting the Pokémon to help them. Ash sends out his Noctowl and Brock sends out his Golbat to help look for Togepi.
In another place, Houndoom is trying to jump over some rocks when an angry Gyarados knocks it into the water. Houndoom struggled with Togepi to get up the shore and this greatly weakens Houndoom as he fell into a short daze. At this time, Togepi tries to climb up a hill, but starts to fall. Houndoom acts fast and saves his little friend. They make their way all the way up to the top of the hill and find a field of flowers with some Grass and Template:Type2 Pokémon. Togepi has some fun, but Houndoom thinks that it is in trouble and tries to save it. The problem is that it makes a Venusaur angry and puts them to sleep.
Back with the gang, Noctowl finds the footprints of Togepi, but there are another set of footprints. Meanwhile, Togepi finally wakes up Houndoom and they get on their way again. Ash and company are hot on Togepi's trail though and they run across the same rocks and see the same Gyarados, but Ash noted it as the young Gyarados. They find a hill and climb up it to find the same field of flowers that Togepi and Houndoom were in earlier.
Team Rocket isn't having very good luck as their patched balloon was leaking air and because of the altitude, they almost crash into the river but banged into an adult Gyrados which pushes them to shore instead. The Gyarados is however enraged and sends them blasting off again with its Water Gun.
Togepi and Houndoom continue to travel further and further. They go inside a tree for shelter during a thunderstorm. Houndoom notices that Togepi was bored and tickled it with it's tail to cheer it up. After the thunderstorm, as they left the tree, near a bush they saw Raikou! It soon jumps away after letting off electric sparks.
Ash and friends seem to have lost Togepi because the footprints have been washed away. They don't give up though and Pikachu finds some fresh footprints. Togepi on the other hand is sleeping on Houndoom's back when it comes back to a farm with an old man with his Mareep. Ash and friends finally catch up and find Togepi! Misty thanks Houndoom for taking care of her Togepi, but then Team Rocket interrupts this happy moment by catching Houndoom in a net. Ash sends out Chikorita again, and it cuts Houndoom free with its Razor Leaf attack. Jessie and James send out Arbok and Victreebel to fight back, but Pikachu and Houndoom save the day and send Team Rocket fire blasting off again, for the third time!
After the battle, the old man leads them back on their way so everyone says goodbye. They start to leave when Togepi starts to cry and runs back to Houndoom. They say a sad goodbye and our heroes continue on their journey.