Ash and his friends find themselves surrounded by a magnificent mountain landscape. As they admire the scenery, they then spot a Houndoom with a satchel on its back as it makes a delivery. Ash checks his Pokédex for further information, and Misty is a little scared of Houndoom's intimidating appearance. Meanwhile, Team Rocket are also enjoying the mountain air from their balloon and take time out to enjoy some tea. They each take a sip when Jessie realizes that they are not fulfilling their required Team Rocket duties. Her teammates also agree, and soon James spots their next target – Ash's Pikachu.
The trio soon put their sneak attack plan into motion and intercept Ash and his friends. Aftering performing their motto, James has his Weezing use Smokescreen, making it impossible for Ash and his 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, Misty trips on a rock and drops Togepi. It rolls near Weezing, so to get away, it uses Metronome, which ends up Teleporting itself far away. Togepi ends up in a big tree and becomes scared after seeing how high off the ground it is. Meanwhile, James commands Weezing to use Tackle. Ash tells Pikachu to do the same, and Weezing is sent flying back into the balloon. Ash calls on Chikorita's assistance, and she cuts a hole through Team Rocket's balloon with a Razor Leaf which sends the evil trio blasting off. Weezing’s Smokescreen finally clears, and Misty informs the others that Togepi is missing. They begin calling out to Togepi, but it is nowhere to be seen.
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. Houndoom sets off again, but Togepi's cries alert it to a Pinsir that is ready to attack. A breath of fire and an intimidating snarl leads Pinsir to walk off. 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. Meanwhile, Misty is becoming increasingly distressed after searching for over an hour for Togepi. Brock urges her to remain calm. He and Ash then send out Noctowl and Golbat to conduct an aerial search for Togepi.
Houndoom continues traveling towards its destination, with Togepi on its back. It reassures Togepi that everything will be okay as it prepares to leaps across several rocks to make it across a raging river. In the midst of the crossing a wild Gyarados breaches the water and the resulting wake swamps Houndoom and Togepi into the river’s current. Houndoom lends its tail to Togepi, who promptly holds on, and the pair soon reach the other side. Togepi proceeds to climb a steep cliff as Houndoom lies exhausted on the riverbank, but it begins to lose its footing. Thankfully, Houndoom notices in time and rescues Togepi before jumping to the top of the cliff in several bounds. Houndoom lets Togepi off and shows it a nearby field of flowers with some Grass and Bug-type Pokémon. Togepi soon joins a trio of Bellossom in dancing. The Bellossom then toss Togepi into the air and it lands on a drowsy Venusaur. The disturbed Pokémon then releases a cloud of Sleep Powder, which Houndoom walk into in order to protect the others.
Back with the gang, Noctowl alerts Ash and his friends to a trail of footprints that resemble Togepi's, but there are another set of larger footprints beside them. Brock notices that Togepi's prints seem to end, while the other larger footprints continue on. Misty is instantly afraid of the thought that Togepi may have been carried away by something. Meanwhile, Togepi finally wakes up Houndoom and they get on their way again. Ash and company are hot on Togepi's trail, and they soon leap across the same rocks and river that Togepi and Houndoom crossed earlier. On the other side of the river the footprints continue, and this leads the group up to the same field of flowers that Togepi and Houndoom were in earlier. Meanwhile, Team Rocket attempt to fly their patched balloon, but it begins leaking air. They almost crash into the river, but Gyarados pushes them to shore instead. The Gyarados is enraged and sends them blasting off again with its Hydro Pump.
Togepi and Houndoom continue to travel further and further. They seek shelter inside a tree hollow as a thunderstorm rages on. Houndoom notices that Togepi is feeling bored and tickles it with its tail to cheer it up. After the thunderstorm has passed, the pair spot a mysterious Pokémon nearby, which leaps away after letting off electric sparks.
Ash and his friends seem to have lost trace of Togepi because the footprints have been washed away by the storm. Soon Pikachu finds some fresh footprints. Misty is somewhat relieved to see that Togepi is still traveling with its mystery companion, and this encourages the group to continue their search. Togepi soon drifts off to sleep on Houndoom's back, as it returns to a Mareep farm. Ash and friends finally catch up and are relieved to find Togepi. Misty thanks Houndoom for taking care of her Togepi, and soon it wakes up and jumps into Misty's arms. The Mareep farmer is glad to see his Houndoom, nicknamed "Doomy", return and he then reaches into the satchel to retrieve his new shears. Team Rocket interrupts this happy moment by catching Doomy 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 blasting off again, for the third time.
After the battle, the Mareep farmer leads Ash's group back to the road towards Ecruteak City. As everyone prepares to say their goodbyes, Togepi begins to cry. It then jumps out of Misty's arms and runs towards Doomy. Doomy smiles at its new friend, but urges Togepi to leave with Misty and the others. Misty promptly picks Togepi up and offers it comfort. Doomy and Togepi share a final goodbye, and afterwards Ash and the others continue their journey.