By taking either the Rainbow or Silver Wing to the Ilex Forest shrine, Gold/Kris travels 150 years back in time to the first day of the fire. It is at this point that we will find out the force behind the lightning bolt that struck the tower.
Witnessing the destruction of the tower, Gold/Kris' objective is to reach the uppermost floor in time to get Lugia
out of harm's way. Lugia
is struggling with its Psychic powers to keep the fire intensity at bay; it cannot continue doing so for long because another force is constantly fueling the flames. Gold/Kris comes to learn that in this time period, Lugia has not yet yet been to the sea, and has thus never mastered the ability to summon rain (Rain Dance). To change this, Gold/Kris forms a bond with Lugia and lets it read their mind, where it sees memories of the Whirl Islands legend; it is this communication that allows Lugia to go about honing Rain Dance. But this process takes time, during which other matters call for immediate action.
For reasons that concern the story up till this point, Gold/Kris has made it their mission to alter the timeline by saving the three nameless creatures from ever dying in the first place (the player has to go through with this decision regardless of whether or not they agree). They do so because they feel that it was through fate that they encountered the three beasts in the basement of the Burned Tower; the legendary beasts have lived a life of solitude obscured from human eye, and the aftermath of being seen in the original incident has the been cause of every selfish act committed by humans against Pokémon - at least in Johto. From this point of view, if the original creatures were to survive the incident and never came to possess legendary powers, the ideal of the towers would live on and humans would never become detached from Pokémon. Surely this must be the reason that Gold/Kris is going through the incident - to change its outcome for the better. Or would it really be for the better?