Lugia, Guardian of the Brass Tower, who represents death, and Houou, Guardian of the Bell Tower, who represents life, reside in the land of Johto. They bring balance to the life between humans and Pokemon.
The residents of Ecruteak City began to pray less as they seem to have grown in interest in the concept of owning Pokemon. An uneasy balance throughout time reaches the residents of Johto. It caused nature to erupt, bringing a heavy storm to Ecruteak City.
A lightning bolt struck the Brass Tower, causing Lugia to fly away to the oceans. The Brass Tower burned for three days until mysterious flood put out the fire. Witnesses say they saw three unknown Pokemon flee from the Bell Tower out of fear. Houou remains at the top of the tower to await the return of its counterpart.
One Ecruteak native by the name of Tojo began to pray inside the now Burned Tower for days after the incident, but saw no progress to summon the abided beast. He sought to once return peace to his home town by embarking on an adventure to track down Lugia and reunite it with Houou.
Weeks go by and Tojo has reached the southwest coast of Johto, where he finds Whirl Island has been split into two lands due to Lugia's rage. Unable to tame the beast on his own, Tojo is approached by Entei and Raikou, who ask of Tojo to join them in a quest to find their friend, Suicune.
Tojo looks back at the day of the disaster and discovers the wild beasts who found him represent the lightning that struck the Brass Tower and the fire which came after. He understands now to restore life back into his home, he must encounter the beast who represents the rain that ended the tragedy.
As he returns home, Tojo finds his people trapped by the Unown, who are threatened by the uneasy nature of humans. They see Tojo with Entei and Raikou, which eases them. The Unown exclaim an exclusive sound that summons the last beast to Ecruteak City. As all three legendary beasts gather outside the Burned Tower, it enables Houou to roar an anicent tune that brings Lugia back to Ecruteak.
As the people begin to pray to their leaders, Tojo is called upon by Suicune to follow it to a new destination. He brings Tojo to the Ilex Forest, where they meet with Celebi, the guardian of the forest, who represents time.
Celebi offers Tojo the opportunity to be brought to different places throughout time to show the legends of his people are in full effect. This helps him understand who he is as the new deity of his town.
Tojo feels compelled to relay the truth back to his people. He has a strong obligation to restore peace to his country and maintain the true balance between humans and Pokemon. His neighbors rejoice to see their guardians have reunited. They immediately begin work to restore Lugia's home at the Brass Tower.
The legendary beasts flee and run wild across the land. They are free of fear and feel comfort in sharing their home with humans. Celebi resides at its home at the Ilex Forest, where Tojo offers his prayers frequently. This brings peace and balance through the land of Johto once again.