- The following is a lore interpretation of the events of Twitch Plays Pokemon Crystal. It is by no means an "official canon", nor is it the only interpretation.
The loric interpretation is that after Lord Helix's victory at the conclusion of Generation 1, Helixism spread throughout Kanto and the Church of Helix was established and began to grow. The Church attempted to expand into the neighboring region of Johto, a region already full of its own spiritual culture. As the Church met with resistance to its spreading influence into Johto, conflicts began to erupt between Church zealots and the population of Johto.
In the revisionist history of Generation 1 and 2 lore, Bill is often credited with sparking the Johto Wars through agents he had planted in the Church. Regardless of Bill's actual involvement, the conflicts that grew out of clashes between the Church and Johto citizens began to grow in scale and violence.
Soon, Helixism dogma also placed certain Pokemon in harms way from Church radicals. Suspicion against Eevees had begun to grow out of fears for the return of The False Prophet, leading capture and confinement of many Eevees, with some lore pointing to Burrito's own capture and confinement being how Bill knew where to send AJ to find him. 'Mon of the Pidgey line were also subjects of prejudice when they were deemed as being "not fit" to be of the line of the savior, Bird Jesus by zealots, leading to Brian's own anger against the Church.
It is believed that AJ, LazorGator (then at Totodile), and the Admiral originally departed to find audience with the Church leadership to plead for an end to the violence, seeking to defeat the eight gym leaders of Johto to gain a pass across the border into Kanto for Pokemon League purposes. However, upon learning of their journey, a small group of extremists within the Church made attempts on LazorGator's life, with the Admiral and eventually Prince Omelette sacrificing themselves instead to protect LazorGator (see full article: The Gator Wars). This is believed to have sparked LazorGator's rage, changing his and AJ's quest to stop the violence the only way they knew how: by taking down the Church's figurehead and god, Lord Helix, who they soon learned was rumored to be residing atop Mt. Silver.
After defeating the gym leaders of both Johto and Kanto, along with the Elite Four, and with a full party of like-minded 'Mon, the group made their way up Mt. Silver to its summit where they faced Helix, Red, and the final party from Generation 1. LazorGator and company were victorious, and Lord Helix's physical form was destroyed, which some interpret as the moment of his ascension.
With its god destroyed and with the world seeing the power of ordinary men and 'Mon, the Church zealots returned to Kanto and dispersed, leaving Johto in peace. In the revisionist history, it is believed that at this time Bill departed the Johto/Kanto regions, and perhaps travelled into the future, with his manipulation of the Church done. In this history, it is believed that Bill instigated the wars to give rise to a godslayer, so that the last of the old-gods would be defeated, leaving him free to move forward with his plans. In classic history and revisionist history, the Church is believed to have dissolved into smaller sects that sought to practice Helixism in peace.